Point cloud data is essential measurement information that has facilitated an extended functionality horizon for urban mobility. While 3D lidar and image-depth sensors are superior in implementing mapping and localization, sense and avoidance, and cognitive exploration in an unknown area, applying 2D lidar is inevitable for systems with limited resources of weight and computational power, for instance, in an aerial mobility system. In this paper, we propose a new pose estimation scheme that reflects the characteristics of extracted feature point information from 2D lidar on the NDT framework for exploiting an improved point cloud registration. In the case of the 2D lidar point cloud, vertices and corners can be viewed as representative feature points. Based on this feature point information, a point-to-point relationship is functionalized and reflected on a voxelized map matching process to deploy more efficient and promising matching performance. In order to present the navigation performance of the mobile object to which the proposed algorithm is applied, the matching result is combined with the inertial navigation through an integration filter. Then, the proposed algorithm was verified through a simulation study using a high-fidelity flight simulator and an indoor experiment. For performance validation, both results were compared and analyzed with the previous techniques. In conclusion, it was demonstrated that improved accuracy and computational efficiency could be achieved through the proposed algorithms.