Specifically for Windblows 98 SE.
I always delete the temp files, cookies and temp internet files and then empty the Recycle Bin before running Spybots Search&Destroy, Ad-Aware and virus scan. But I notice that these programs will wade through a ton of temp internet files anyway. Search the folders and the files are empty. One day I right clicked Temp I-net folder and it said I had over 1 gig in it. Funny, nothing was showing on the inside. Yes, I view hidden files. So MicroShaft has a double secret hidden file system. Just how to reveal and delete them was the question.
Answer: Start-Find Files or Folders-Temporary Internet Folders\Content\IE
Once found I had to highlight and delete each folder manually. Took some time but I recovered over a Gig of space on my C drive.