Using the module (XML::Twig) really is the easiest way to do it:

use strict;
use warnings;
use XML::Twig;

my $xml = <<XML;
<?xml version="1.0" encoding="UTF-8"?>
<Node_A>
    <!-- One Line Comment -->
    <Node_B>
        <!-- Two Line Comment
Two Line Comment-->
        <Node_C>
        </Node_C>
        <!-- One Line Comment -->
        <!-- Multi  Line Comment
  Line 3Comment
  1Line Comment
  2Line Comment
  Line 5Comment
Line Comment-->
    </Node_B>
</Node_A>
XML

my $twig = XML::Twig->new (comments => 'drop', pretty_print => 'indent
+ed');

$twig->parse ($xml);
$twig->print ();
[download]

Prints:

<?xml version="1.0" encoding="UTF-8"?>
<Node_A>
  <Node_B>
    <Node_C></Node_C>
  </Node_B>
</Node_A>
[download]