If it's getting to the point where this workstation computer is going to need to go into command line for manual deletion of files, then why not save the time and effort and simply reformat?
Why settle for a plethora of spyware infections that may or may not leave the system insecure/unstable after their removal, when you could take that mass hazard and simply wipe it clean? Normally I wouldn't recommend this, as I've cleaned boxes with 2,000 counts of spyware/adware. But if the spyware gets rooted deep enough into the system, lots of it, then you can't trust the registry stability any longer nor the system stability if it altered/replaced windows specific files that you had to delete.
