#!/perl/bin/perl
use strict;
use warnings;
use Template;

my $template = Template->new();
my $str = "some [% foo.bar %] stuff\n";
$template->process(\$str,
        { 
        foo => { bar => 'cool' },
        }) or warn $template->error;
__END__
some cool stuff
[download]

Maybe you shouldn't use the same string for both input and output (that appends the result to the template, at least in my tests).