open( LIST, "mystopwords.txt" ) or die "$!";
my @stopwords = <LIST>;  # assuming one stop word per line
close LIST;
chomp @stopwords;

my $stopregex = join '|', @stopwords;

# ... now, when you go to delete stopwords from $_,
# it goes like this:

   s/\b(?:$stopregex)\b//g;