A minimally invasive surgical system includes a pair of surgical instruments having end effectors to hold and suture tissue, a pair of robotic arms coupled to the surgical instruments, a controller, and a pair of master handles coupled through the controller to the robotic arms, so that surgeon manipulation of the handles produces corresponding movement of the end effectors in an adjustably scaled fashion. An input button allows the surgeon to adjust the position of the handles without moving the end effectors, so that the handles may be moved to a more comfortable position. An optionally included robotically controlled endoscope allows the surgeon to remotely view the surgical site. Using the system, a cardiac procedure can be performed by making small incisions in the patient's skin, inserting the instruments and endoscope through the incisions, and manipulating the handles to move the end effectors to perform the cardiac procedure.