### No reason to do this, since you could just use the filename in the "open" call directly.
my $executable = "C:/Users/Desktop/file.exe";

### This won't work - that "-w" is extraneous and a syntax error. Furthermore, you have a conceptual problem:
### the way you're doing it here (if it worked) would OVERWRITE your program instead of
### executing it.
open(-w EXECUTABLE,">$executable") or die "Can't open output file $executable\n";
while(<EXECUTABLE>) {
    print EXECUTABLE "Something";
}
close EXECUTABLE;