Perhaps it would be better it iterate through the files like so

foreach my $file ($f, $a, $scratchfile, $fasta_output) {
    if(-e $file) {
        print "Files belonging to a previous version exist\n";
        unlink $file;
    } else {
        ...
    }
}
[download]

Also note you don't have to quote the filenames like you might in a shell script as perl Does The Right Thing.
HTH

_________
broquaint