After reading the Wordpress documentation, I realized you can remove posts from the index using filters inside "The Loop", e.g.:
<?php if ( have_posts() ) : while ( have_posts() ) : the_post(); ?>
<!-- The following tests if the current post is in category 3. -->
<?php if (in_category('3')) continue; ?>
<!-- display normal post -->
<?php endwhile; else: ?>
<p>Sorry, no posts matched your criteria.</p>
<?php endif; ?>
What I'm wondering is if there is a filter/hook to filter posts in have_posts()
without modifying the template. So far, I found options to change the results, but not remove results form the result set.