tell us your not physically going in & deleting files on your own. you should be using the programs Uninstall process/file to uninstall the proper files. or at the very least using Windows Add/Remove program.
Personally I wouldn't touch any of those files your talking about unless you are absolutely certain they aren't needed...
if you delete the wrong files many times that can seriously hose your entire Operating system. usually leaving them is preferred over losing all data & reinstalling your OS. if the files your talking about are in the Folder or directory that was made for the Antivirus program itself, then that might be ok to delete, but if the files your talking about are in one of Windows Folders, then leave it.