A system for registering a luminal network of the airways to a 3D model of the luminal network comprising: a generator for generating an electromagnetic field about the luminal network; a location sensor responsive to the electromagnetic field to produce location data; and a processing system configured to carry out the steps of: generating a 3D model of a luminal network based on images of the luminal network; tracking the location of the location sensor within the luminal network using location data acquired from the location sensor in the electromagnetic field; comparing the tracked locations of the location sensor with sensors located outside of the luminal network and the portions of the 3D model representative of open space; and presenting on a user interface an indication of which lung portions of the luminal network have been sufficiently traversed by the location sensor to register those lung portions of the luminal network to the 3D model, wherein the processing system requires the location sensor to be navigated to the second bifurcation of each airway passage of a lung portion in order for the lung portion to be sufficiently traversed; and wherein the processing system is configured to determine (308, 314) that a done button for ending the acquistion of location data has been activated and, if so, to determine whether the acquired location data points are substantially located within the luminal network of the 3D model, and if not, restart the registration of the luminal network to the 3D model. a generator for generating an electromagnetic field about the luminal network; a location sensor responsive to the electromagnetic field to produce location data; and a processing system configured to carry out the steps of: generating a 3D model of a luminal network based on images of the luminal network; tracking the location of the location sensor within the luminal network using location data acquired from the location sensor in the electromagnetic field; comparing the tracked locations of the location sensor with sensors located outside of the luminal network and the portions of the 3D model representative of open space; and presenting on a user interface an indication of which lung portions of the luminal network have been sufficiently traversed by the location sensor to register those lung portions of the luminal network to the 3D model, wherein the processing system requires the location sensor to be navigated to the second bifurcation of each airway passage of a lung portion in order for the lung portion to be sufficiently traversed; and wherein the processing system is configured to determine (308, 314) that a done button for ending the acquistion of location data has been activated and, if so, to determine whether the acquired location data points are substantially located within the luminal network of the 3D model, and if not, restart the registration of the luminal network to the 3D model. generating a 3D model of a luminal network based on images of the luminal network; tracking the location of the location sensor within the luminal network using location data acquired from the location sensor in the electromagnetic field; comparing the tracked locations of the location sensor with sensors located outside of the luminal network and the portions of the 3D model representative of open space; and presenting on a user interface an indication of which lung portions of the luminal network have been sufficiently traversed by the location sensor to register those lung portions of the luminal network to the 3D model, wherein the processing system requires the location sensor to be navigated to the second bifurcation of each airway passage of a lung portion in order for the lung portion to be sufficiently traversed; and wherein the processing system is configured to determine (308, 314) that a done button for ending the acquistion of location data has been activated and, if so, to determine whether the acquired location data points are substantially located within the luminal network of the 3D model, and if not, restart the registration of the luminal network to the 3D model.