A medical robotic system has a surgeon console which is operatively couplable to a patient side unit for performing medical procedures or operatively couplable to a simulator unit for training purposes. The surgeon console has a monitor, input devices and foot pedals. The patient side unit has robotic arm assemblies coupled to instruments and an endoscope. When the surgeon console is coupled to the patient side unit, the instruments move in response to movement of the input devices to perform a medical procedure while captured images of the instruments are displayed on the monitor. When the surgeon console is coupled to the simulator unit, virtual instruments move in response to movement of the input devices to perform a user selected virtual procedure while virtual images of the virtual instruments are displayed on the monitor.