How are you seeing the C: drive if it is blank? If the C: drive was accually empty, you wouldn't be in windows. I'm thinking the malware is showing you some fake stats. Can you boot into safe mode? If you can you can run MalwareBytes or a similar program to remove some of the bad files.
If you can't boot into safe mode, you can boot into the system with a liveCD (hirem's boot CD, UBCD) and run anti-malware programs from there.
Safemode is your first stop right now.
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Formatting and reloading is the last possible step, that's like dropping a nuke on a house to kill a spider.
Boot into safe mode (with networking if you can) and download
http://www.malwarebytes.org/ if you can, update and run. Should fix (most) problems. If that step doesn't work, we will go to step two and download you a live boot CD to fix it.