1. A system for navigating a medical instrument within a branched structure of a body, the system comprising: a tracking system for collecting information defining a position of the medical instrument with respect to a frame of reference of the tracking system; and a workstation including a database, a processor and a display, the processor coupled to the database and coupled to the tracking system, to receive the positional information therefrom, and the display coupled to the processor; the database including data, which defines a geometrical model of the branched structure, the data including coordinates for predetermined points, with respect to a model coordinate system in a frame of reference of the model, the predetermined points defining a pathway along branches of the model of the branched structure and including a designated point, serving as a reference point for the model coordinate system, and a plurality of other designated points; the processor adapted to: receive input for establishing an anchor point of a coordinate system for the frame of reference of the tracking system, the anchor point corresponding to the first designated point of the pathway; convert the positional information, collected by the tracking system, into Euclidean distances of the instrument from the established anchor point of the tracking coordinate system; identify sets of coordinates of the instrument for each Euclidean distance of the instrument from the established anchor point that corresponds to a Euclidean distance of one of the plurality of other designated points, of the pathway, from the reference point of the model coordinate system; register the tracking coordinate system to the model coordinate system by deriving a mathematical transformation, which relates the model frame of reference to the tracking frame of reference, using the identified sets of coordinates of the instrument and the corresponding coordinates of the plurality of other designated points of the pathway; and map locations of the instrument to the pathway by continuing to convert positional information for the instrument into Euclidean distances from the established anchor point of the tracking coordinate system, following registration of the tracking coordinate system to the model coordinate system; and the display adapted to receive data from the database, to display a representation of the model, to receive mapped locations of the instrument, from the processor, and to display the mapped locations of the instrument, on the representation of the model.