open my $input, "<", $ARGV[0] or die "couldn't open $ARGV[0]: $!";
open my $output, ">", "output.txt" or die "coudln't open output: $!";
while(<$input>) {
    if( m/something/ ) {
        # do stuff
    }
    s/stuff//g; # etc.

    print {$output} $_;
}
close $output;
close $input;