A method comprises identifying connected anatomical structures in stored images of a patient anatomy and generating a first three-dimensional model of anatomic passageways including a set of anatomical centerlines of the anatomic passageways, and generating a second three-dimensional model of the anatomic passageways including a plurality of linkage elements each including two base points defining a linkage element centerline spanning a shortest distance between the two base points. The method also comprises receiving tracking data corresponding to a point on an instrument positioned within the connected anatomical structures, matching the point on the instrument to one of the plurality of linkage elements representing one of the connected anatomical structures to locate the instrument relative to the connected anatomical structures in the stored images of the patient anatomy, and updating the matching of the point on the instrument to one of the plurality of linkage elements.