Three-dimensional indoor navigation requires various functions, such as the shortest path retrieval, obstacle avoidance, and secure path retrieval, for optimal path finding using a geometrical network model. Although the geometrical network model can be prepared manually, the model should be automatically generated using images and point clouds to represent changing indoor environments. Thus, we propose a methodology for generating a geometrical network model for indoor navigation using point clouds through object classification, navigable area estimation, and navigable path estimation. Our proposed methodology was evaluated through experiments using the benchmark of the International Society for Photogrammetry and Remote Sensing for indoor modeling. In our experiments, we confirmed that our methodology can generate a geometrical network model automatically.