Lots of malware can not be cleaned from an active drive (ie. you've booted into Windows). You should remove the drive and either install it in an external USB enclosure or install as a second drive on a known, proven clean, system.
There you can scan the entire contents of the disk without any of the files being "live". Best is to scan with multiple anti-virus (means multiple clean machines) and malware scanners.
This is the only way (short of wiping and reinstalling) to be reasonably certain of getting it all.
This is how I do it in my shop and I'm 99%+ successful.