The invention comprises a virtual window system that creates a visual coherency between the image of the patient and his or her anatomy and the patient by aligning the image of the patient anatomy on the display to the patient and presenting the image to the user that feels as if the user is looking directly into the patient through the display. The invention is designed to also display medical devices, such as a minimally invasive tool. The system substantially unifies the coordinate systems of the patient, the medical device, the display, and the physician's hands. The invention creates a visual coherency between the motion of the medical device in the image and the motion of the physician's hands manipulating the device. This invention also creates a visual coherency between the motion of the image in the display and of that display.