Methods and systems for registering a manipulator assembly and independently positionable surgical table are provided herein. In one aspect, methods include attaching a registration device to a particular location of the surgical table and attaching a manipulator arm of the manipulator assembly to the registration device and determining a position and/or orientation of the surgical table relative the manipulator assembly using joint state sensor readings from the manipulator arm. In another aspect, methods for registration include tracking of one or more optical or radio markers with a sensor associate with the manipulator assembly to determine a spatial relationship between the surgical table and manipulator assembly.
