Vehicle self-localization techniques, such as GNSS and Velodyne, can benefit greatly by accessing to an accurate 3D building map, especially in urban areas. Though, an accurate automatic 3D building map reconstruction is challenging in dense urban areas, in which buildings are located close to each other. In general, 3D building map can be generated from adding accurate height information of the building roofs to a detailed 2D map. But 2D building maps usually only provide footprint of the buildings which is not enough for 3D shape modeling of complicated buildings in urban areas such as Shinjuku, Tokyo, Japan. On the other hand, with the development of laser scanning technology, airborne laser scanning (ALS) has now become easily accessible for large scale 3D mapping. However, an automatic 3D map reconstruction using only airborne point cloud is not feasible for dense urban areas, because of the difficulty of defining boundary of each building individually. This paper presents an automatic 3D building map reconstruction technique which integrates airborne laser point cloud with 2D boundary map. Results from Shinjuku area is evaluated for the proposed technique.