strict is your friend. :) It's telling you that you need to explicitly scope $filename and @rows. Try this:

my @rows;

if (@files)
{
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    foreach my $filename(@files){

      $filename = substr($filename,0,-4);

      my $sth = $cbh->prepare("SELECT id, title, summary FROM  resourc
+e WHERE id =?");
      $sth->execute($filename);

        while (my $ref = $sth->fetchrow_hashref()){

        my $title = $ref->{title};
        my $id = $ref->{id};

        push @rows, { ID => $id, TITLE => $title };

    }
  }
}

my $template = HTML::Template->new(filename => 'ee_search.tmpl');

$template->param(SEARCH_STRING => $search);
$template->param(ROWS => \@rows);
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-Matt