Systems, methods, and computer-readable media for registering initial computed tomography (CT) images of a luminal network with subsequent CT images of the luminal network include obtaining initial CT images of the luminal network and subsequent CT images of the luminal network, generating an initial three-dimensional (3D) model of the luminal network based on the initial CT images of the luminal network, generating a subsequent 3D model of the luminal network based on the subsequent CT images of the luminal network, matching the initial 3D model with the subsequent 3D model based on a registration, and performing geometric filtering and/or topological filtering on the matching of the initial 3D model and the subsequent 3D model. In various embodiments, a thin plate splines transformation from the initial 3D model to the subsequent 3D model is derived based on portions of the initial 3D model and the subsequent 3D model that were matched by the matching and that remain matched after the geometric filtering or the topological filtering.
