Stone tools are valuable archaeological findings dating to prehistoric age. The ancient people hit a rock with a stone hammer to make stone tools, it also produces flakes. To analyze human activities, reassembling stone tools is effective. When these stone tools are assembled using a computer, the flake surfaces of each stone must be extracted. The segmentation process is necessary for reassembling. This study aims for the segmentation in order to extract flake surfaces, and it requires identifying the orientation of the point normal vector. To do this, the surface of a flake must be considered. If the external space of the object can be correctly defined, directing normal vector is sufficient. While the surface is defined by adopting the voxelization technique, a surface is determined by a voxel that contains points. In addition, external and internal voxels are identified using the 3D flood filling algorithm. We applied normal vector estimation to region-growing segmentation and confirmed its effectiveness experimentally.