Removing custom post type name in single article URLs

Use the post_type_link hook, like this for use hash in link

faq is the example custom post type

add_action( 'post_type_link', 'wpse70763_post_type_link', 10, 2 );
function wpse70763_post_type_link( $link, $post ) {

    $post_type="faq";

    if ( $post->post_type === $post_type )
        $link = get_post_type_archive_link( $post_type ) . '#' . $post->post_name;

    return $link;
}

then unset($wp_rewrite->extra_permastructs['faq'])

On the init of your CPT unset the pemastructure