A system for registering an initial three-dimensional model of a luminal network based on an initial computed tomography images of a luminal network with a subsequent 3D model of said luminal network based on subsequent CT images of the luminal network, the system comprising: a computing device including a processor and a memory; an application, stored in the memory and executed by the processor, which when executed, causes the computing device to: a) obtaining initial CT images of the luminal network and subsequent CT images of the luminal network; b) generating an initial three-dimensional model of the luminal network based on the initial CT images of the luminal network; c) generating a subsequent 3D model of the luminal network based on the subsequent CT images of the luminal network; d) matching the initial 3D model with the subsequent 3D model based on a registration between the initial 3-D model and the subsequent 3-D model; and e) unmatching portions of the initial 3D model and of the subsequent 3D model that do not satisfy a matching threshold; and f) registering the initial 3D model with the subsequent 3D model based on portions of the initial 3D model and of the subsequent 3D model that remain matched after the unmatching; where wherein matching the initial 3D model with the subsequent 3D model based on a registration comprises: selecting a plurality of initial reference points within the initial 3D model; and selecting a plurality of reference points within the subsequent 3D model, wherein the plurality of initial reference points and the plurality of reference points include x, y, and z coordinates. a computing device including a processor and a memory; an application, stored in the memory and executed by the processor, which when executed, causes the computing device to: a) obtaining initial CT images of the luminal network and subsequent CT images of the luminal network; b) generating an initial three-dimensional model of the luminal network based on the initial CT images of the luminal network; c) generating a subsequent 3D model of the luminal network based on the subsequent CT images of the luminal network; d) matching the initial 3D model with the subsequent 3D model based on a registration between the initial 3-D model and the subsequent 3-D model; and e) unmatching portions of the initial 3D model and of the subsequent 3D model that do not satisfy a matching threshold; and f) registering the initial 3D model with the subsequent 3D model based on portions of the initial 3D model and of the subsequent 3D model that remain matched after the unmatching; where wherein matching the initial 3D model with the subsequent 3D model based on a registration comprises: selecting a plurality of initial reference points within the initial 3D model; and selecting a plurality of reference points within the subsequent 3D model, wherein the plurality of initial reference points and the plurality of reference points include x, y, and z coordinates. a) obtaining initial CT images of the luminal network and subsequent CT images of the luminal network; b) generating an initial three-dimensional model of the luminal network based on the initial CT images of the luminal network; c) generating a subsequent 3D model of the luminal network based on the subsequent CT images of the luminal network; d) matching the initial 3D model with the subsequent 3D model based on a registration between the initial 3-D model and the subsequent 3-D model; and e) unmatching portions of the initial 3D model and of the subsequent 3D model that do not satisfy a matching threshold; and f) registering the initial 3D model with the subsequent 3D model based on portions of the initial 3D model and of the subsequent 3D model that remain matched after the unmatching; where wherein matching the initial 3D model with the subsequent 3D model based on a registration comprises: selecting a plurality of initial reference points within the initial 3D model; and selecting a plurality of reference points within the subsequent 3D model, wherein the plurality of initial reference points and the plurality of reference points include x, y, and z coordinates. selecting a plurality of initial reference points within the initial 3D model; and selecting a plurality of reference points within the subsequent 3D model, wherein the plurality of initial reference points and the plurality of reference points include x, y, and z coordinates.