If the file is not checked out, clearcase will not allow you to modify it. I'm not sure if File::Copy will return any error messages, but it wouldn't hurt to check. I'm not sure of the syntax (for File::Copy) either, so I can't really tell you if that's right.
Perl also has chmod built in. Try copying with File::Copy and then
chmod 0644, $file or warn "Unable to chmod $file!\n$!\n";