1. A method for operating a medical robotic system, the method comprising: receiving intraoperative external image data for at least a portion of a patient anatomy, the intraoperative external image data comprising image data for a target location in the patient anatomy; and at least semi-automatically controlling a medical instrument of the medical robotic system based on the intraoperative external image data to deliver a substance to the target location through the medical instrument of the medical robotic system.