That code could be prettier, but it has a serious bug in it:

    # if you want to delete, make the line with null value;

    $data[$line] = "";
[download]

This doesn't actually delete the line; it replaces it with an empty line. Oh, and there's another bug -- why join lines on newlines when you haven't chomped away existing newlines? Here's much better code:

my $filename = 'yourfilename.txt';
my $newfile  = 'new_filename.txt';

filter_file( $filename, $newfile );

# this line may be unnecessary depending on your filesystem
unlink $filename;
rename( $filename, $newfile );

sub filter_file
{
    my ($from, $to) = @_;
    open my $fh,          $from or die "Can't read '$from': $!\n";
    open my $out_fh, '>', $to   or die "Can't write '$to': $!\n";

    while (<$fh>)
    {
        next if should_delete_line($_);
        print {$out_fh};
    }
}
[download]