You'd have to open an input and an output file — generally they're not the same one, unless you're very clever about it.

There is actually an example on the page I linked but it may have been unobvious to locate.

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;
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