<?php
    //pre_get_posts filter is called before WordPress gets posts
    add_filter( 'pre_get_posts', 'my_get_posts' );

    function my_get_posts( $query ) {
        //if page is an archive and post_parent is not set and post_type is the post type in question
        if ( is_archive() && false == $query->query_vars['post_parent'] &&  $query->query_vars['post_type'] == 'my_post_type')
            //set post_parent to 0, which is the default post_parent for top level posts
            $query->set( 'post_parent', 0 );
        return $query;
    }
    ?>