A system includes a medical instrument, a teleoperation manipulator, an optical tracking sensor, and a control system. The medical instrument includes an elongated flexible body, a rigid proximal body comprising a reference portion, and a shape sensor having a reference point. The control system is configured to: track, with the optical tracking sensor, a first set of optical fiducials on a patient anatomy and a second set of optical fiducials on the reference portion; determine, using the second set of optical fiducials, a position of the reference point for a plurality of insertion measurements of a position measuring device; receive shape information from the shape sensor; and determine a pose of a portion of the elongated flexible body with respect to the patient anatomy using the first set of optical fiducials, the position of the reference point as indicated by the position measuring device, and the shape information.