$data = q`
HTML1
<% CODE1 %>
HTML2
<% CODE2 %>
HTML3
<p>foo</p>
`;

use Data::Dumper;
use HTML::TokeParser;
my $parser = HTML::TokeParser->new( \$data );
while ( my $token = $parser->get_token() ) {
    print Dumper($token) if $token->[1] =~ m/<%/;
}

__DATA__
$VAR1 = [
          'T',
          '<% CODE1 %>
HTML2
',
          ''
        ];
$VAR1 = [
          'T',
          '<% CODE2 %>
HTML3
',
          ''
        ];