3D modeling of functional buildings is growing rapidly because of its excellence. 3D modeling can also be applied to heritage buildings, but it is still rarely done due to the variety of detail, and the unique shape of the objects in heritage buildings make it more difficult to be modeled. In consequence, an adequate instrument with different scanning densities is required in this case, namely Terrestrial Laser Scanner (TLS) and Handheld Laser Scanner (HLS). This study, conducted at Penataran Temple in Penglipuran Village, Bali, aims to analyze the registration result of point clouds acquired by TLS and HLS, as well as its capability to build the 3D model. Point cloud data is acquired using TLS and HLS tools, and the information about the object is obtained by doing interviews with the Chief of Penglipuran Village and the villagers. The point cloud that TLS acquires is registered with Iterative Closed Point (ICP) algorithm, while the point cloud of HLS is registered by using Helmert and Affine transformation method. Based on the results, the registration of HLS point cloud data to the TLS Affine method has better quality accuracy than the Helmert method. In addition, point cloud data scanned by HLS can present 3D models with a better Level of Detail (LOD) than point cloud data from TLS.