How about something simple?

use autodie;
while (<>)
{
    last if /^__END__/;
    next if /^\s*#/;
    ...;
}
[download]

Now, the same functionality implemented with the guidelines.

(Since this is Perl, I am adapting the guidelines to encompass Perl concepts.)

my $EndOfInput = 0;
for my $file (@ARGV)
{
    if (0 == $EndOfInput)
    {
        if (open(my $fh, '<', $file))
        {
            while (my $line = <$fh>)
            {
                if (0 == $EndOfInput)
                {
                    if ($line =~ /^__END__/)
                    {
                        $EndOfInput = 1;
                    }
                    else
                    {
                        if ($line !~ /^\s*#/)
                        {
                            ...;
                        }
                    }
                }
            }
        }
        else
        {
            die "Can't open $file: $!"; # we are allowed to die on fat
+al errors
        }
    }
}
[download]