A medical robotic system provides 3D telestration over a 3D view of an anatomical structure by receiving a 2D telestration graphic input associated with one of a pair of stereoscopic images of the anatomical structure from a mentor surgeon, determining a corresponding 2D telestration graphic input in the other of the pair of stereoscopic images using a disparity map, blending the telestration graphic inputs into respective ones of the pair of stereoscopic images, and providing the blended results to a 3D display so that a 3D view of the telestration graphic input may be displayed as an overlay to a 3D view of the anatomical structure to an operating surgeon.
