You want to use a different loop variable in your inner-loop; and then bind the substitution to $line:

  foreach my $line (@words) {
    $line =~ tr/A-Z/a-z/;
    foreach my $ignore (@ignore) {
      $line =~ s/\b$ignore\b//;
    }
  }
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I've also added \b assertions around the word that you're ignoring, to prevent strange modifications in the middle of words. --Dave