A system and method for navigating a medical instrument in a branched structure of a body employs a tracking system, for collecting positional information for the medical instrument, and data, which defines a geometrical model of the branched structure, in particular, coordinates for predetermined points defining a pathway extending along branches of the model. Coordinates are identified for each Euclidean distance of the instrument, from an anchor point of a coordinate system for the tracking system, that corresponds to a Euclidean distance of a designated point, of the predetermined points, from a reference point of a coordinate system for the model, wherein the anchor point of the tracking coordinate system has been established to correspond to the reference point of the model coordinate system. The two coordinate systems are registered to one another using the identified coordinates of the instrument and the corresponding coordinates of each designated point.