You're often better off pulling the drive and scanning from another system, or other OS install or USB booted cleaner on the same. You don't get the registry cleaned that way but can remove some files which could have a protection setup that relaunches them if terminated and/or reinstalls them. Once you're sure you have a clean environment with no malware that would run, then and only then would I boot that windows install to finish cleaning up.
Make note of the dates of the files. Look for other files created near the same time. Scanners don't always catch everything but if there are alien files you can at least quarantine them by moving, renaming, and ultimately deleting them if windows and your apps run okay without them.
Something else you can do beforehand is make a partition image. If things go sideways and windows won't boot then you can choose between restoring that, doing a repair install or a clean one, and have a recent backup of your other files in the process.