Malware removal - Am I done?

My method for cleaning malware is to pull the hard drive and attach it as a slave to a Windows 7 machine.  Then I boot  Windows 7 and run Kaspersky on the questionable drive. After Kaspersky finds a bunch of Trojans and Java exploits. I run "M.S. Stand-Alone-Scanner" and often it  finds a bunch more Trojans and Java exploits. This makes me wonder what I might find if I run other Anti-Virus programs that might find stuff that Kaspersky and "M.S. Stand-Alone-Scanner" did not find.

Sometimes the malware changes the registry settings and I need to use Combo Fix.

Is there a better method I can use to assure I have cleaned up all the malware?

How do I know when a system is clean?
scottjnorrisAsked:
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HaslerctConnect With a Mentor Commented:
Rule of thumb... When the system infected by malware before, reformat it! There is no 100% "way" other than this...

Unless you use all anti malware/virus scanner available in the world... As every vendor have their own anti malware pattern and that's why some can detect some cannot.

Cheers...
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John HurstBusiness Consultant (Owner)Commented:
Once you put the system back into operation, run the online Malwarebytes to see if it finds yet more stuff.

Once a system is infected (especially if it gets a rootkit), there is no guarantee you got it all. But what you did plus Malwarebytes is at least a very good attempt. See what happens after a day or two.

.... Thinkpads_User
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Scott ThompsonComputer Technician / OwnerCommented:
Malwarebytes is a great suggestion. Also, you can run TDSSKiller slaved, but only with the functions 'Detect TDLFS System' and 'Scan Boot Sectors'. Great for removing pesky rootkits.
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Dave BaldwinFixer of ProblemsCommented:
On all serious infections I start with ComboFix followed by Malwarebytes.  Sometimes I have to use a Linux Live disk to find and remove the main virus program first so I can load those two programs.
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abolinhasCommented:
Try kaspersky rescue disk
https://support.kaspersky.com/4131
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