Malware Attack (Help): Windows folders are missing

I got hit with a malware attack last week. I have a Windows PC (I think Windows 2000). I've used several software downloads to remove it, but I'm not convinced it is gone. When I go into Google, I get redirected. Something is still there. The system is slow and isn't working right. Sometimes it takes up to 30 minutes to get into Explorer.

While I'm still working to get rid of it, all of the folders disappeared during the attack (e.g., Accessories, games, MS applications (Word, Project, etc), ability to restore, defrag, paintbrush, etc), Burn a CD and so on. When I go to Start/Programs, the only thing there is what has been added since the attack. The applications seem to work (e.g., I can get into Word), the folders are just missing or hidden. In addition, I can't right click on a picture anymore and make it a background wallpaper.

Any ideas on how to get these back?

Thanks for any help you can offer.