A medical system provides navigation assistance to a surgeon so that the surgeon may navigate a flexible medical device through linked passages of an anatomical structure to a target in or adjacent to the anatomical structure. As the medical device moves through the linked passages, images are captured by an image capturing element at its distal end and pose and shape information for the medical device are received from sensors disposed in the medical device. A 4-D computer model of the anatomical structure is registered to the medical device using one or both of 4-D shape registration and virtual camera registration so that the captured image and a virtual image generated from the perspective of a virtual camera are registered to each other and displayed while providing an indication of a navigational path to the target.