You can't do that.
If you copy a file, the destination file is exactly the same as the original - it does not contain any information which says "I am the third copy of xxx" or anything like that. If you ship a setup program and I copy it before I install it, it doesn't matter what you do to the original when I install it, I still have the copy which I can install from because it is untouched.
Look instead at copy protecting your application through licencing: Software Copy Protection for .Net Applications - a Tutorial
] but don't expect miracles! Adobe spend millions on copy protecting Photoshop, and the "cracked" version hits the torrent sites the same day they release a new version!