As you can learn from your example with sort, the external command takes your lines from the standard input.

Change your script this way:

#!/usr/bin/perl -w
use strict;

while (<>) {
    chomp;
    print "file is [$_]\n";
    if ( ! -e $_ ) {
        print  "#$_\n";
    } else {
        print "$_\n";
    }
}
[download]

However, if your Vim has direct Perl support, you can execute something like this:

:1,$ perldo s/^/#/ unless -e $_
[download]

See Editing features for advanced users for an explanation and more examples on similar features.

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