In one embodiment of the invention, a method for a minimally invasive surgical system is disclosed. The method includes capturing and displaying camera images of a surgical site on at least one display device at a surgeon console; switching out of a following mode and into a masters-as-mice (MaM) mode; overlaying a graphical user interface (GUI) including an interactive graphical object onto the camera images; and rendering a pointer within the camera images for user interactive control. In the following mode, the input devices of the surgeon console may couple motion into surgical instruments. In the MaM mode, the input devices interact with the GUI and interactive graphical objects. The pointer is manipulated in three dimensions by input devices having at least three degrees of freedom. Interactive graphical objects are related to physical objects in the surgical site or a function thereof and are manipulatable by the input devices.