A medical robotic system comprising: an image capturing device for capturing images; a robotic arm holding the image capturing device; a computer display screen; a master input device adapted to be manipulatable by a user in multiple degrees-of-freedom movement; and a processor configured to: when the master input device is in an image capturing mode, control movement of the image capturing device according to user manipulation of the master input device; and when the master input device is in an image manipulating mode: control the displaying of images derived from the captured images on the computer display screen according to user manipulation of the master input device; characterized by the processor further configured to: display one of the three-dimensional volumes and a two-dimensional window on the computer display screen; manipulate a position and orientation of the window on the computer display screen in response to user manipulation of the master input device; and define a cut-plane by an intersection of the window with the three-dimensional volume so as to indicate a two-dimensional slice of the three-dimensional volume. an image capturing device for capturing images; a robotic arm holding the image capturing device; a computer display screen; a master input device adapted to be manipulatable by a user in multiple degrees-of-freedom movement; and a processor configured to: when the master input device is in an image capturing mode, control movement of the image capturing device according to user manipulation of the master input device; and when the master input device is in an image manipulating mode: control the displaying of images derived from the captured images on the computer display screen according to user manipulation of the master input device; characterized by the processor further configured to: display one of the three-dimensional volumes and a two-dimensional window on the computer display screen; manipulate a position and orientation of the window on the computer display screen in response to user manipulation of the master input device; and define a cut-plane by an intersection of the window with the three-dimensional volume so as to indicate a two-dimensional slice of the three-dimensional volume. when the master input device is in an image capturing mode, control movement of the image capturing device according to user manipulation of the master input device; and when the master input device is in an image manipulating mode: control the displaying of images derived from the captured images on the computer display screen according to user manipulation of the master input device; characterized by the processor further configured to: display one of the three-dimensional volumes and a two-dimensional window on the computer display screen; manipulate a position and orientation of the window on the computer display screen in response to user manipulation of the master input device; and define a cut-plane by an intersection of the window with the three-dimensional volume so as to indicate a two-dimensional slice of the three-dimensional volume. control the displaying of images derived from the captured images on the computer display screen according to user manipulation of the master input device; characterized by the processor further configured to: display one of the three-dimensional volumes and a two-dimensional window on the computer display screen; manipulate a position and orientation of the window on the computer display screen in response to user manipulation of the master input device; and define a cut-plane by an intersection of the window with the three-dimensional volume so as to indicate a two-dimensional slice of the three-dimensional volume. display one of the three-dimensional volumes and a two-dimensional window on the computer display screen; manipulate a position and orientation of the window on the computer display screen in response to user manipulation of the master input device; and define a cut-plane by an intersection of the window with the three-dimensional volume so as to indicate a two-dimensional slice of the three-dimensional volume.