How to Know If Your Computer Is Infected

These days malicious software is becoming an epidemic. It seems like it’s everywhere. Also, sadly, there's been a change in the way malware acts. It used to be that it would slow down your computer, or display annoying popups, but now malware is becoming increasingly discreet. You could be infected right now and not even know it. Also, sadly, it often seems as if the only way to make sure you’re not infected is to scan your computer with numerous anti-malware programs. Doing this can be time consuming and, while scanning, may even slow your computer to a crawl. Even after that you still can’t be sure you're clean. This is because scanners cannot recognize all new malware.
Because of these difficulties I have come up with a better method. This uses multiple programs, not to remove files, but just to analyze the computer. Each of these programs is very effective and easy to use. They are all portable applications and will not cause any conflicts on your computer because they are only running when you're using them. However, they do require an active internet connection to function properly. Don't worry, this guide will also help you to fix your internet connection in the event that it is not working. After you have already gone through the below process once, and had all files whitelisted, this approach is much faster, much more certain, and much easier than any other approach I've seen. No active malware can escape this process. However, inactive pieces of malware may not be flagged by this approach but may be found by other scanners. Rest assured that these are not direct threats to the safety of your computer and thus do not constitute a failure of this article.
This article is meant for those who believe it's possible, but are not sure, that malware is running on their computer. The reason I say that is that some malware will immediately start doing things such as encrypting files. Thus, the longer your computer is running in normal mode the greater the damage will be. However, if you only have fleeting suspicious that something may be amiss on your computer I recommend that you follow the below advice to find out for sure.
I also want to stress that in order to make sure that your computer is not infected you must follow each step. None is meant to be used independently. Each depends on the others to account for different infection scenarios. 

1. What To Do If Computer Is Unbootable

Note that if your computer is able to boot into Windows you should skip directly to the next section. However, if your computer is not able to boot into Windows I would first advise that you follow the advice I give in this section of an article I wrote about How to Fix a Malware Infected Computer. It may be able to help make your computer bootable again. Then, once it's fixed, you can begin following the advice in the next section to see if your computer is infected.
Note that if the advice in that section of the other article is not able to fix your problems you should not follow part D in that article, but instead follow the advice given in this section of an article I wrote about How to Clean An Infected Computer. It's possible that the reason that your computer cannot boot is because of malware. Thus cleaning it may be the only way to get the computer running again.

2. Check for Rootkits

It's important to ensure that there are no active rootkits on your computer. To do this first scan your computer with Kaspersky TDSSKiller. It can be downloaded from this page. Note that if the file from that link is not working correctly try right-clicking on it and choosing to Save As. If even this doesn't work then you can instead download a zip file containing the same scanner from this page. At this same time download the zip file for Comodo Cleaning Essentials from this page.  Make sure to select the correct version for your operating system. If you're not sure if your computer is running a 32 or 64 bit operating system then please see this FAQ. Note that if neither will not download correctly, or your internet connection is not working, you should download them on another computer and transfer them to the infected one via a flash drive. Make sure there were no other files on the flash drive. Be careful with the flash drive as the malware may actually infect it when you plug it into the computer. Thus, don't plug it into any other computers after transferring these programs.
Kaspersky TDSSKiller will scan your computer for some of the most common types of rootkits. I've found it to have relatively few false positives and a very high detection rate. By the way, some scanners, including Comodo Cleaning Essentials, may detect this file as a dangerous file. It is not. This is a safe download link. If it is flagged as dangerous you can safely ignore the detection. As with every program in this article, I recommend that you do not quarantine any files using this program. A false positive on the wrong file could destroy your computer, even if you’re not infected.
To use this it open the file called TDSSKiller. Then select the option to “Start Scan”. This scan should take less than a minute. If it does find anything then it's likely that your computer is infected. However, if you believe the detected files are not dangerous you can investigate them to see if they are false positives. 
Unzip the folder for CCE. Then double click on the file called CCE. This will open the main program for Comodo Cleaning Essentials. If it refuses to open then hold down the shift key and, while still holding it down, double click on the file called CCE. After CCE has successfully opened you can let go of the shift key. However, do not let go of it until the program has fully loaded. If you let go of it even during the UAC popup it may not be able to forcefully open correctly. Holding down shift should allow it to open, even on heavily infected computers. It does this by killing most of the unnecessary processes that could be interfering with its launch. If it still will not launch then download and run a program called RKill. This can be downloaded from this page. This program will terminate known malicious processes. Thus, after running it CCE should be able to open fine. Do not remove or disable anything with CCE as it can be very dangerous if used improperly. We are only using its analytical abilities. Please do not use it to try and clean up any infections or you could inadvertently harm your computer.

Now select the option to do a smart scan with CCE. It will immediately begin downloading the most recent virus database, which may take a long time to complete. Once it has completed downloading, the scan will begin immediately. This will scan your computer for all types of malware.  The scan should not take too long to complete. As before, I recommend that you do not quarantine any files using this program. One problem with this program is that I do find it to have a few false positives. Thus the best option, in order to be sure of the results from its scan, is to report any files detected as dangerous, which you believe may be safe, to Comodo for analysis.
Sadly there is no easy way to navigate to the files detected by the scan. You will have to manually navigate to the path indicated in the scan results in order to get to them. Note that if you do not want to investigate them right now you can select the option to ignore each detection. Then allow finish and restart your computer. Next time you open CCE you can go to "Tools" and choose "Browse logs". The detections you chose to ignore, along with their file paths, should be stored in the most recent log. To report the detected files as false positives you should go to this page. Then select false positive, upload the files in question, fill out the required information, and select submit. Comodo analysts will send you an email with the results of their analysis.
This program also scans for system changes which may have been caused by malware. These will also be shown with the results. If you did not make these changes yourself then this could possibly be evidence that there is malware on your computer. I would recommend letting CCE fix these items, but not anything else, and continuing with the rest of the article to see if there is any more evidence of infection. I would not consider unwanted system modifications to be definitive evidence of an infection.
After the scan is complete it will ask you to restart your computer. Allow it to restart. Do not open any unnecessary programs as this will make the next step simpler. Once again I will remind you to not quarantine any files with this program. Once it restarts it will pop up with the final results. 

3. Use KillSwitch

A) Use KillSwitch To Investigate Running Processes
If the above steps did not find any malware activity then you should again open Comodo Cleaning Essentials (CCE). However, this time you should go to "Tools" and select the option to "Open KillSwitch". KillSwitch which will immediately begin analyzing all of your running processes. This analysis should only take a minute or so. Without waiting for the analysis to complete you can go to “View” and select “Hide Safe Processes”. This will hide all processes that are verified to be safe by Comodo. The reason I asked you not to open any other programs in the above step is because malware will nearly always run on system startup, while many legitimate programs will not. Thus there will be fewer processes to examine.
Once the analysis is complete all that are left are those programs which are either believed to be dangerous or are not in Comodo's whitelist. The latter type is denoted as FLS.Unknown. Be aware that unknown does not mean dangerous. It only means that the file has not yet been whitelisted by Comodo.
B) Analyze KillSwitch Results
If KillSwitch now shows that “There are no items to show”, then your computer passed this part of the tests. If there are files remaining in the list then you should investigate them. In order to do this you first need to navigate to the files. To do this right click on the process in question and select “Jump to Folder”. This will open up the folder where the associated file is located and select the file as well.
For files which are flagged as dangerous or suspicious, but which you believe may actually be safe, I would recommend that you report them as a false positive on this page. Just select false positive and fill out the required information. Comodo analysts will get back to you by email with the results of their analysis. In this way you can easily find out for sure if the files really are dangerous or not.
C) Submit Unknown Files Which Are Probably Safe To Comodo For Whitelisting
For those files which are flagged as FLS.Unknown, but which you believe are probably safe, the most efficient way to analyze them is to submit them to Comodo for whitelisting. Instructions for how to submit programs, or individual files that belong to programs, can be found in this topic of the Comodo forum. Make sure you read through the first post entirely and follow all recommendations. This will ensure that your request is completed as quickly as possible. However, do note that in order to submit programs, or files, you do need to have an account on the Comodo forums. If you don't already have one then it's very easy to get one. There is an option to register on the top of any page on the Comodo forums. Also, if you cannot locate the folder indicated in the KillSwitch results that may be because some folders are hidden by default by Windows. To tell Windows to show you those folders please follow the advice on this page.
These submissions will be analyzed by Comodo staff and, if appropriate, added to the whitelist. However, do note that it may take the analysts days, or even a few weeks, to complete their analysis. This all depends on how many submissions they are also trying to analyze. 
That said, the greatest advantage to the whitelisting approach is that you won't have to do any analysis of your own and the next time you check your computer the files will already be whitelisted and nothing will need to be done. In fact, you submit all the safe programs on your computer for whitelisting then, once they're whitelisted, the next time you scan with KillSwitch there should not be any more unknown processes for you to examine. Thus, it becomes an incredibly easy task to ensure that your computer is still clean of infections. In fact, my computer always shows a completely blank screen after selecting the option to “Hide Safe Processes”. This allows me to ensure that my system has passed this test in less than one minute. Please note that depending on your computer, and your internet connection speed, this time may vary. Once you're done with this part you can close KillSwitch.

4. Use Comodo Autoruns

A) Use Comodo Autoruns To Investigate Registry Entries
Now, through CCE, which should still be open, again go to the "Tools" menu. This time select the option to "Open Autorun Analyzer". This program will analyze the registry and show you the files associated with each item. Almost all malware will write to the registry. Thus, by scanning for all files associated with registry entries, this program can identify malware and unknown files, even if they aren't running. It may even be useful in identifying rootkits, although that is not its primary purpose. The downside to using this program is that it will potentially give you more files to check than the above methods. However, if you really want to be sure that your computer is clean then this step is also necessary. As before, do not delete/disable anything with this program as it can be very dangerous if used improperly. We are only using its analytical abilities. Please do not use it to try and clean up any infections or you could inadvertently harm your computer.
After Comodo Autoruns opens it will immediately begin compiling the list. This process could take a couple of minutes to complete. Without waiting for the list to finish being compiled you can go to “View” and select “Hide Safe Entries". Note that this option will now be pre-checked every subsequent time you run the program. Once the list is compiled Comodo Autoruns will automatically begin analyzing each entry. Wait until all entries have been analyzed. If this is the first time you have run this program, you should now close it and then open it again. I find that this often allows Comodo time to analyze some of the unknown files so that this time there will be less to check.
If Autoruns now shows that “There are no items to show” your computer passed this part of the tests. If it also passed all of the above steps then there is definitely no active malware on your computer.
If your computer passed all of the above steps, but you are experiencing problems with your computer, it's possible that the problem that you're experiencing is due to hardware or software issues. I would recommend that you first try searching online for symptoms similar to what your computer is suffering from to see if they match something other than malware. It was written mainly to fix probelms due to malware, but the advice given should be able to fix many other types of software problems as well.
B) Analyze Comodo Autoruns Results
However, if there are still entries left over you should begin analyzing them. However, note that there is currently a minor bug with Comodo Autoruns. This sometimes causes the program to flag files which are actually known safe as FLS.Unknown. Thus, I would advise that if you see many files flagged as unknown, which you believe should be flagged as safe, that you close Comodo Autoruns and then open it again to see if the files are still unknown. Also, note that making sure the virus database is fully up to date, by always running a Smart Scan with CCE just before checking with Comodo Autoruns, makes this problem much less rare.
To get to the files which these entries are associated with, right click on an entry and select “Jump to Folder”. This will open up the folder where the associated file is located and select the file as well. Also, with this program you will find that often a single file has numerous entries, which means that often there’s not nearly as much analysis to be done as there would seem to be.
Just as was done for KillSwitch, for files which are flagged as dangerous or suspicious, but which you believe may actually be safe, I would recommend that you report them as a false positive on this page. Just select false positive and fill out the required information. Comodo analysts will get back to you by email with the results of their analysis. In this way you can easily find out for sure if the files really are dangerous or not. Also, if you cannot locate the folder indicated in the results that may be because some folders are hidden by default by Windows. To tell Windows to show you those folders please follow the advice on this page.
C) Submit Unknown Files Which Are Probably Safe To Comodo For Whitelisting
For those files which are flagged as FLS.Unknown, but which you believe are probably safe, the most efficient way to analyze them is to submit them to Comodo for whitelisting. Instructions for how to submit programs, or individual files that belong to programs, can be found in this topic of the Comodo forum. Make sure you read through the first post entirely and follow all recommendations. This will ensure that your request is completed as quickly as possible. However, do note that in order to submit programs, or files, you need to have an account on the Comodo forums. If you don't already have one then it's very easy to get one. There is an option to register on the top of any page on the Comodo forums. Also, if you cannot locate the folder indicated in the Autoruns results that may be because some folders are hidden by default by Windows. To tell Windows to show you those folders please follow the advice on this page.
These submissions will be analyzed by Comodo staff and, if appropriate, added to the whitelist. However, do note that it may take the analysts days, or even a few weeks, to complete their analysis. This all depends on how many submissions they are also trying to analyze. 
That said, the greatest advantage to the whitelisting approach is that you won't have to do any analysis of your own and the next time you check your computer the files will already be whitelisted and nothing will need to be done. In fact, you submit all the safe programs on your computer for whitelisting then, once they're whitelisted, the next time you scan with Comodo Autoruns there should not be any more unknown processes for you to examine. Thus, it becomes an incredibly easy task to ensure that your computer is still clean of infections. In fact, my computer always shows a completely blank screen after selecting the option to “Hide Safe Entries”. This allows me to ensure that my system has passed this test in just a few minutes. Please note that depending on your computer, and your internet connection speed, this time may vary.

5. How To Clean Infections From Computer

If any of these methods does show that your computer is infected you should check out my article about How to Clean An Infected Computer. The advice in this article will allow you to remove almost any infection and get your computer back to working order.