Apparently it can't be done if you're aiming in stylus mode. That or it's either so precise that you shouldn't even bother. That's what I've been told anyway (I've never tried). What you need to do is after it is done attacking, freeze it, and then lock on to a joint with the a button. Shoot it with your attack move until it turns red. Now it can't be damaged anymore. Once all the joints are red, you can lock on to the Harvester proper and attack.