A system includes a manipulator and a processing unit. The processing unit is configured to receive, from a position sensor system, a collected set of spatial information for a distal portion of a medical instrument collected at locations within anatomic passageways as a rigid instrument body is moved in an insertion or retraction direction. The processing unit is further configured to receive, from a position measuring device, a set of position information related to a position of the rigid instrument body when the distal portion is at the locations. The processing unit is further configured to, based at least in part on the set of position information, determine a subset of the set of spatial information relative to the environment coordinate space and, based on the subset of spatial information, determine an initial transform for registering the set of spatial information with anatomical model information in a model coordinate space.