Methods and systems for registering a manipulator assembly and independently positionable surgical table are provided herein. In one aspect, methods include reading a fiducial marker on the surgical table with a sensor associated with the manipulator assembly and localizing the manipulator assembly and surgical table with respect to a common reference frame. Methods may further include translating a 3D configuration of the surgical table to a 2D frame of reference so as to estimate a 3D pose of the surgical table relative to the manipulator assembly for use in coordinating movements therebetween.