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We propose some methods to automatically estimate the position of orbitale and tragion from raw 3D scanner data. The 3D scanner captures point cloud and mesh data representing the body surface. To utilize the data, we also need underlying anatomical landmarks. The tragion position is estimated using three methods, by detecting the saddle shaped area, by setting an average position relative to ear robe, and by 3D template matching. Orbitale position is estimated by regression analysis using the position of eyes and subnasale as independent variables. The methods are tested and the results are compared using 20 Japanese head form data.