A sub-system configured for use in a medical robotic system, the medical robotic system comprising: a medical instrument; and a robotic arm coupled to the medical instrument; the sub-system comprising: a handle adapted to be gripped and manipulated by a hand of a user, the handle having a multi-function button positioned on the handle so as to be depressable by the user without removing their hand from the handle; a computer screen displaying a graphical user interface for user selection of a selected function for the multi-function button from a plurality of user selectable functions of the medical robotic system including a motion scaling function, wherein the motion scaling function allows the user to vary motion scaling of the medical robotic system with the multi-function button and wherein motion scaling varies the corresponding movement of the handle and the medical instrument; an input device associated with the graphical user interface so as to allow user selection of one of the plurality of user selectable functions identified on the computer screen; and a controller configured to couple with the robotic arm and the handle, and configured to control robotic movement of the medical instrument by the robotic arm in response to user manipulation of the handle. a medical instrument; and a robotic arm coupled to the medical instrument; the sub-system comprising: a handle adapted to be gripped and manipulated by a hand of a user, the handle having a multi-function button positioned on the handle so as to be depressable by the user without removing their hand from the handle; a computer screen displaying a graphical user interface for user selection of a selected function for the multi-function button from a plurality of user selectable functions of the medical robotic system including a motion scaling function, wherein the motion scaling function allows the user to vary motion scaling of the medical robotic system with the multi-function button and wherein motion scaling varies the corresponding movement of the handle and the medical instrument; an input device associated with the graphical user interface so as to allow user selection of one of the plurality of user selectable functions identified on the computer screen; and a controller configured to couple with the robotic arm and the handle, and configured to control robotic movement of the medical instrument by the robotic arm in response to user manipulation of the handle. a handle adapted to be gripped and manipulated by a hand of a user, the handle having a multi-function button positioned on the handle so as to be depressable by the user without removing their hand from the handle; a computer screen displaying a graphical user interface for user selection of a selected function for the multi-function button from a plurality of user selectable functions of the medical robotic system including a motion scaling function, wherein the motion scaling function allows the user to vary motion scaling of the medical robotic system with the multi-function button and wherein motion scaling varies the corresponding movement of the handle and the medical instrument; an input device associated with the graphical user interface so as to allow user selection of one of the plurality of user selectable functions identified on the computer screen; and a controller configured to couple with the robotic arm and the handle, and configured to control robotic movement of the medical instrument by the robotic arm in response to user manipulation of the handle.