David wants to know how malware effects reinstalling apps. Leo says that once he strips off the malware, he'll have to reinstall his apps. The only way to be sure that he's eliminated the malware is to backup his data, wipe his drive and reinstall Windows. How about an image of the drive? As long as he has a clean image, he could use that. If his computer has malware when he makes the image, he'll just restore the malware. Leo would wipe the drive, reinstall everything, update it all, and then make an image.
Imaging options include: