When a large number of stone tools need to be studied, a unique identification number is assigned to each stone tool to distinguish one from the others. Since most of the current methods of stone tool management are operated manually, identification information may be lost in the process of research. Therefore, a new system is required to provide the identification numbers automatically from actual stone tools. The previous study proposed an identification method that realizes matching using stone tool silhouettes and the ICP algorithm. However, it is difficult to identify stone tools if they are thick because the matching method is based on two-dimensional approach. According to Chida et al., the improvement of performance is achieved using D2 distribution to narrow down candidates as a preprocessing step for stone tool matching. This paper proposes a method that realizes matching including D2 distribution, which enables 3D comparison, with the methods of the previous study to achieve higher identification accuracy.