Use XML::Twig or XML::TreeBuilder. Life is not long enough to roll your own XML/HTML/CSV parser. To get you started:

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

my $twig = XML::Twig->new();

$twig->parse (do {local $/; <DATA>});

my @chunks = $twig->root ()->children();
my %lookup;

for my $chunk (@chunks) {
    my $words = $chunk->first_child ('words');
    my $text = $words->xml_text ();
    push @{$lookup{$_}}, $chunk for split /,\s+/, $text;
}

#do stuff with %lookup

__DATA__
<doc>
    <MS_1>
      <loc>c:\data\cat.xml</loc>
      <words>dog, cat, fish, bird</words>
    </MS_1>
    <MS_2>
      <loc>c:\data\cow.xml</loc>
      <words>dog, cat, fish, bird, cow, goat</words>
    </MS_2>
    <MS_3>
      <loc>c:\data\snake.xml</loc>
      <words>dog, cat, fish, bird, snake, orange</words>
    </MS_3>
</doc>
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