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while (my $line = <$original_fh>) {
    print "Enter the desired number of columns: ";
        my $nr = <STDIN>;
...
    $line =~ s/(\d{2})/$replace[$1]/g;
    print $final_fh $line;
}

 while (my $line = <$original_fh>) {
    for my $file (@files) {
    print "Enter the desired number of columns: ";
...
    print $final_fh $line;

  }