A medical robotic system comprising: a driver assembly configured to operate a medical instrument; a master assembly for controlling the driver assembly; a memory to receive intraoperative external image data for at least a portion of a patient anatomy, wherein the portion of the patient anatomy is an anatomical feature positioned within the patient anatomy, and wherein the intraoperative external image data comprises image data for a target location in the patient anatomy and for an effect of a substance on the target location; a display system for displaying the intraoperative external image data; and a processor configured to: at least semi-automatically control the medical instrument of the medical robotic system based on the intraoperative external image data to deliver the substance to the target location through the medical instrument of the medical robotic system by adjusting a control parameter for delivering the substance based on the intraoperative external image data; identify image data for the substance in the intraoperative external image data and display the image data for the substance on the display system; identify one or more features of the patient anatomy in the intraoperative external image data; and intraoperatively generate an updated model of the patient anatomy by applying a modeling adjustment to an existing model of the patient anatomy, wherein the existing model is missing one or more anatomical structures, wherein the modeling adjustment is based on the identified one or more features of the patient anatomy, and wherein applying the modeling adjustment includes adding a model of the one or more missing anatomical structures to the existing model of the patient anatomy, wherein the identified one or more features of the patient anatomy include the one or more missing anatomical structures. a driver assembly configured to operate a medical instrument; a master assembly for controlling the driver assembly; a memory to receive intraoperative external image data for at least a portion of a patient anatomy, wherein the portion of the patient anatomy is an anatomical feature positioned within the patient anatomy, and wherein the intraoperative external image data comprises image data for a target location in the patient anatomy and for an effect of a substance on the target location; a display system for displaying the intraoperative external image data; and a processor configured to: at least semi-automatically control the medical instrument of the medical robotic system based on the intraoperative external image data to deliver the substance to the target location through the medical instrument of the medical robotic system by adjusting a control parameter for delivering the substance based on the intraoperative external image data; identify image data for the substance in the intraoperative external image data and display the image data for the substance on the display system; identify one or more features of the patient anatomy in the intraoperative external image data; and intraoperatively generate an updated model of the patient anatomy by applying a modeling adjustment to an existing model of the patient anatomy, wherein the existing model is missing one or more anatomical structures, wherein the modeling adjustment is based on the identified one or more features of the patient anatomy, and at least semi-automatically control the medical instrument of the medical robotic system based on the intraoperative external image data to deliver the substance to the target location through the medical instrument of the medical robotic system by adjusting a control parameter for delivering the substance based on the intraoperative external image data; identify image data for the substance in the intraoperative external image data and display the image data for the substance on the display system; identify one or more features of the patient anatomy in the intraoperative external image data; and intraoperatively generate an updated model of the patient anatomy by applying a modeling adjustment to an existing model of the patient anatomy, wherein the existing model is missing one or more anatomical structures, wherein the modeling adjustment is based on the identified one or more features of the patient anatomy, and wherein applying the modeling adjustment includes adding a model of the one or more missing anatomical structures to the existing model of the patient anatomy, wherein the identified one or more features of the patient anatomy include the one or more missing anatomical structures.