Remove default subpages from Custom Post Menu

You can manipulate the global variable $submenu and remove them. In normal circumstances, the index key values are 5 (All items) and 10 (New item). In this example, the post type is portfolio:

add_action( 'admin_init', 'remove_cpt_submenus_wpse_95797' );

function remove_cpt_submenus_wpse_95797()
{
    global $submenu;
    unset(
        $submenu['edit.php?post_type=portfolio'][5], 
        $submenu['edit.php?post_type=portfolio'][10] 
    );
}