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I downloaded MSE and finally detected all the problems none of the antivirus programs would ... turns out I had 29 exploit viruses and 5 trojans thanks to a program I downloaded a while back ... most of it pertains to Java and I haven't been able to goof off on the computer like i enjoy. I'm sure I know how to fix the problem, but the removal of the viruses is take a long time. I'm going into my 3rd day of waiting for them to be removed. Do I need to be nervous or just sit back and let it do what it does?

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I cannot believe that it takes 3 days. I wouldn't be nervous but I would cancel and try again. –  Xavierjazz Jun 29 '12 at 18:27

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You computer was probably too infected to deem safe anymore. The removal should defiantly not take that long and since you have been infected so long you probably have a rootkit.

Per Microsoft's recommendation for major malware infections:

Once you've identified a rootkit on your system, the remediation options are somewhat limited. Because rootkits can hide themselves, you may not know how long they've been on the system. You also may not know what information the rootkits have compromised. The best reaction to an identified rootkit is to wipe and reinstall the system. Although drastic, this is the only proven method to completely remove rootkits.

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I'd add that these days, once you have a confirmed malware infection odds are good enough that the infection brought a rootkit along for the ride to warrant jumping right to the wipe/reinstall phase. The risk of an unknown keylogger/credential stealer remaining behind are too great. –  Joel Coehoorn Jun 29 '12 at 19:04
    
@JoelCoehoorn Malware is vicious these days. –  Jeff F. Jun 29 '12 at 19:27

I would try a couple things - first, make sure that your virus definitions are up to date, reboot into Safe Mode and re-run MSE. Then, reboot normally, download ComboFix, and run it, as it seems to handle rootkits very well.

If after that, things still do not seem right, download a bootable, updateable antivirus live cd, like BitDefender Rescue CD with auto-update, boot to it, and re-scan your system.

Worst case scenario, wipe your machine, restore your system, and start over. This, of course, may be the healthy option as your machine may never run the same again once infected.

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On a system with known infections you should only run malware scans from well defined clean environments. So just skip the first steps and start with a live CD. Since there will still be a risk remaining, just reinstalling/restoring from a clean backup is the only reliable solution. –  Gurken Papst Jun 29 '12 at 19:25

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