1. A method for a minimally invasive surgical system, the method comprising: capturing one or more camera images of a surgical site; displaying the one or more captured camera images of the surgical site on at least one display device at a surgeon console; switching out of a following mode in which one or more input devices of the surgeon console are used to couple motion into minimally invasive surgical instruments and into a masters-as-mice mode in which the one or more input devices are used to interact with a graphical user interface; overlaying the graphical user interface including an interactive graphical object onto the one or more captured camera images displayed on the at least one display device at the surgeon console, wherein the interactive graphical object is related to a physical object in the surgical site or a function thereof and is manipulated by the one or more input devices of the surgeon console in the masters-as-mice mode; and rendering a pointer within the one or more captured camera images displayed on the at least one display device for user interactive control of the interactive graphical object, wherein in the masters-as-mice mode the pointer is manipulated in three dimensions within the one or more captured camera images by at least one of the one or more input devices of the surgeon console having at least three degrees of freedom.