Yes, you would have to pull off the eye caps. If the eye caps doesn't come off with the shed, then you would have to pull them off. I haven't had this problem yet, but I have assisted a shed and pulled off eye caps before. After each time a snake sheds, the eye caps should come off with the rest of the shedding. If the shedding was incomplete, the humidity was most likely not at the correct level, resulting in an incomplete sheds and possibly the eye caps did not come off.