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Are you saying that by removing the TEMP files you will remove viruses from Windows 2000? I'm not sure that will be sufficient in most cases.
TEMP files can be safely erased. I run batch files which erase all of these files and folders each night. This is a good part of regular system maintenance.
However, I also run regular virus scans of my entire PC. A lot of viruses make changes to your Registry, so using a simple registry protector that alerts you to any changes and requests your permission for each change is often a good defense.