A pretty good spyware article here, came up with some good stuff:
There are two main ways of getting rid of malicious software programs from an infected Microsoft windows install: with the contaminated windows OS working or not.

The easy way, of course, is from within just the contaminated windows installation. Just download anti-malware software package, install it, run it and get on with life. The issue is, you may not be able to get into your install to use it properly.

The two massive downsides to a clean set up are shedding the installed programs and all user personal data. Making an attempt to backup all of the records and data ahead of wiping the entire disk thoroughly clean is an accident waiting to take place. You are bound to overlook something. One particular way to insure that all data is completely backed up is to make a complete disk image backup. There are several apps which do this easily, and some of them are even free.

Even with out disk impression backup deal, it is feasible to do a cleanse set up of your windows programs and also conserve the infested duplicate of Windows (not for the functions necessarily but to insure that you have all your information saved). How? Through disk partitions. You can preserve the old copy of windows in 1 partition and put in the new, fresh, completely clean duplicate in a distinctly separate partition.

When operating the freshly minted duplicate of Microsoft windows, the aged and infested backup can either be visible to it. Once it is visible, then information information can be copied from it to the new Windows instance as the user requires. First though, you should use anti-virus and anti-spyware  software to thoroughly clean the old copy of windows to eliminate the malware from the backup. If you think you've cleaned out the old windows install, then you may want to boot it to to test it out. Just be sure to clean everything out and be ready for a complete failure, just in case.