1. A system for positioning a surgical instrument relative to a patient's body, comprising: a robotic manipulator having at least one controlled degree of freedom; a controller controlling the robotic manipulator; an instrument holder attaching a first surgical instrument to the robotic manipulator; a second surgical instrument held by a surgeon; a surgeon input device mounted on the second surgical instrument, the surgeon input device permitting the the surgeon to specify desired motions of the first surgical instrument to the controller so that the robotic manipulator moves the first surgical instrument to a position relative to the patient's body as specified by the surgeon using the surgeon input device.