Slave the drive out to anther boot, by making another boot drive master, or booting to Linux Live (or bartPE). Then try to clean. If trying to run inside windows from own drive/ not slaved out some stuff will be running that could block, rebuild on fly etc. Safe mode is safest for this strategy; as less will be running. Other malware/virus tricks would be to not let you run known anti-malware apps. Then in that case, i would download the app on another sys, and rename it, then bring to your sys. Some of the newer malware can get around this by tracking by process thread name and stopping, instead of by file name and stopping. This is another reason not booting to the suspect drive is best.
Would always recomend backup- infected backup can be better than no backup. If can't beat, and can't get in, can also try a dual installation next to old win install, then boot to it, then get info off, then do real install. If malware is suspected and reinstalling for that reason, it is also wise to wipe out any partitions for diagnostics etc. that manufacturer places on drive, to kill any infections there. Also, recommend the non-Fast NTFS formatting for this. If not having to reinstall and get fixed; and sure everything is okay, recommend turning off system restore, boot, then turn it back on, to further fight reinfection.