May I suggest that you need to create a new file, commenting out the required line/s, then rename it? For example:

use warnings;
use strict;

my $filename = 'C:/oracle/ora81/network/ADMIN/SQLNET.ORA';

open (my $in, '<', $filename) || die "Unable to open $filename:$!";
open (my $out,'>', "$filename.tmp") || die "Unable to open $filename.t
+mp:$!";

while (<$in>) {

    # Identify the record
    if ($_ eq "SQLNET.AUTHENTICATION_SERVICES= (NTS)\n"){
        $_ = '# '.$_;
    }

    print $out $_;
}

close $in;
close $out;

rename "$filename.tmp",$filename or die "Unable to rename: $!";
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