prad, some suggestions:

1. Give those temp vars meaningful names.. What are they? Found files? folders? Ah, MD5s.. then call them $tempMD5_1 or something..
2. Don't copy code unless you know what it does. I get the feeling you copied that if(($file1 eq $file2) =~(/.zip/i)){ or similar from somewhere.
3. Try to explain yourself in words what the code does
4. Use debugging prints. Print out what $file1 is, what $file2 is, what ($file1 eq $file2) is, and finally the entire expression in the if. Then you'll see why it doesnt work.

C.