open (my $in, "<", $ARGV[0]) 
    or die "in: $@";

open (my $out, ">", "$ARGV[0].new") 
    or die "out: $@";

while( my $line = <$in>)
{
    print $out $line
        unless $line =~ /^#/;
}

close $in;
close $out;

##</code><code>##

open (my $in, "<", $ARGV[0]) 
    or die "in: $@";

my @lines = grep { not /^#/ } <$in>; #<> here in list context, therefore no explicit loop