A method of continuously registering a model of anatomic passageways to a patient space includes: collecting a set of measured points along a flexible catheter as the catheter is inserted into the passageways, the measured points based on a shape of the catheter; assigning each measured point to a respective subset of a plurality of subsets based upon a depth of each measured point within the passageways; comparing the plurality of subsets to identify a first optimal subset; registering the model to the patient space based on a set of model points and the first optimal subset; collecting additional measured points; updating the plurality of subsets by assigning each additional measured point to a respective subset; comparing, after the updating, the plurality of subsets to identify a second optimal subset; and registering the model to the patient space based on the set of model points and the second optimal subset.