Use the post_link
filter hook:
add_filter( 'post_link', 'wpse_change_post_link', 99, 3 );
function wpse_change_post_link( $url, $post, $leavename = false ) {
// Can't fill these conditions since you didn't specify them...
if ( 'my_post_type' === $post->post_type ) {
$url=""; // Your new URL...
}
return $url;
}