A medical system comprising: a flexible instrument including a sensor (136, 138) adapted to provide tracking data for a point on the instrument; a memory storing images of a patient anatomy; and a processor configured for identifying connected anatomical structures in the stored images of the patient anatomy; said processor being characterized in that it is further configured for: generating an anatomic centerline model from a series of centerpoints through the connected anatomical structures; generating a bounding surface model including a plurality of cylindrical linkage elements representing the connected anatomical structures, each cylindrical linkage element including a bounding surface determined from and formed around a branch of the anatomical centerline model, wherein the bounding surface for each cylindrical linkage element in the bounding surface model is formed at a radial distance from the branch of the anatomical centerline model; receiving the tracking data corresponding to the point on the instrument positioned within at least one of the connected anatomical structures; and matching the point on the instrument to one of the plurality of cylindrical linkage elements by determining one or more cylindrical linkage elements, of the plurality of cylindrical linkage elements, closest to position coordinates of the point on the instrument. a flexible instrument including a sensor (136, 138) adapted to provide tracking data for a point on the instrument; a memory storing images of a patient anatomy; and a processor configured for identifying connected anatomical structures in the stored images of the patient anatomy; said processor being characterized in that it is further configured for: identifying connected anatomical structures in the stored images of the patient anatomy; said processor being characterized in that it is further configured for: generating an anatomic centerline model from a series of centerpoints through the connected anatomical structures; generating a bounding surface model including a plurality of cylindrical linkage elements representing the connected anatomical structures, each cylindrical linkage element including a bounding surface determined from and formed around a branch of the anatomical centerline model, wherein the bounding surface for each cylindrical linkage element in the bounding surface model is formed at a radial distance from the branch of the anatomical centerline model; receiving the tracking data corresponding to the point on the instrument positioned within at least one of the connected anatomical structures; and matching the point on the instrument to one of the plurality of cylindrical linkage elements by determining one or more cylindrical linkage elements, of the plurality of cylindrical linkage elements, closest to position coordinates of the point on the instrument. generating a bounding surface model including a plurality of cylindrical linkage elements representing the connected anatomical structures, each cylindrical linkage element including a bounding surface determined from and formed around a branch of the anatomical centerline model, wherein the bounding surface for each cylindrical linkage element in the bounding surface model is formed at a radial distance from the branch of the anatomical centerline model; receiving the tracking data corresponding to the point on the instrument positioned within at least one of the connected anatomical structures; and matching the point on the instrument to one of the plurality of cylindrical linkage elements by determining one or more cylindrical linkage elements, of the plurality of cylindrical linkage elements, closest to position coordinates of the point on the instrument.