Not sure if I fully understand but I think what you are saying is you have used a aplication that will delete all ocurances of Internet Explorer from your computer but now you notice your hidden files are gone

Firstly what hiden files are gone? maybe they had something to do with IE so the software just took it out. Were they your own files or do you know for a fact that they were not part of IE.

I know that IE has files all over your computer, And I would expect some of them to be marked as hidden.

Can you give me the name of the program you used to remove IE and I can check it out for you, Also my friend would also like to get rid of IE from his computer, so the name of the program would be helpfull.