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How do I get rid of malicious spyware, malware, viruses or rootkits from my PC?

I recently identified some suspicious CPU activity on my Windows 7 x64. While idle in task manager top processes consume about 5-7% of CPU, but in Performance tab I can see about 25-30% consumption. With my i5 Intel (2 cores / 4 threads) this suggest, that there is running single thread app consuming whole core, but it is not listed in Task Manager.
I have scanned computer with Windows Defender and Avast, but they found nothing.

Any ideas how to track, what process is consuming so much CPU?

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High CPU usage can mean a number of things. It might not be a virus at all, could just be a faulty process (had that on my Mac the other day - bloody parentalcontrolsd). Best thing is to use Task Manager to see which process is causing it (make sure it shows processes for all users, not just you). If that doesn't work out, use Process Monitor for more detailed information on your running processes.

Failing that, restart your PC in Safe Mode (press F8 just before the Windows logo shows up). See if it still happens.

Another thing to check is your startup items, go to Start > Run (or Ctrl-R) and type in msconfig. Go to the Startup tab and see what items are being loaded on boot, maybe uncheck some, restart and try again.

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Task Manager by default won't show services or other system processes. So what you see as the “top processes” is just the “top usermode processes that you started” (or running in your session). Try clicking the Show processes from all users button to see the rest:

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Most often there is some service doing background activity. It could be your malware scanner currently scanning or the indexing service.

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