It would seem you are going about this the hard way. Instead of breaking the sentences down into words you could combine the stopwords and make a regex.

Then you just use s/// to replace occurences of the stop words with nothing or a marker of some sort.

use strict;
use warnings;

my $text = "Hello world how are you doing?";
my @stopwords = ("hello","how");
my $regex = join('\b|\b', @stopwords);
$text =~ s/$regex/*BAD*/igs;
print $text;
[download]