A fundamental prerequisite for safe and efficient navigation of mobile robots is the availability of reliable navigation maps upon which trajectories can be planned. With the increasing industrial interest in mobile robotics, especially in urban environments, the process of generating navigation maps has become of particular interest, being a labor intensive step of the deployment process. Automating this step is challenging and becomes even more arduous when the perception capabilities are limited by cost considerations. This paper proposes an algorithm to automatically generate navigation maps using a typical navigation-oriented sensor setup: a single top-mounted 3D LiDAR sensor. The proposed method is designed and validated with the urban environment as the main use case: it is shown to be able to produce accurate maps featuring different terrain types, positive obstacles of different heights as well as negative obstacles. The algorithm is applied to data collected in a typical urban environment with a wheeled inverted pendulum robot, showing its robustness against localization, perception and dynamic uncertainties. The generated map is validated against a human-made map.