In this paper, we present a 3D reconstruction method of color volume data for a computerized human atlas. Binary volume rendering which takes the advantages of object-order ray traversal and run-length encoding visualizes 3D organs at an interactive speed in a general PC without the help of specific hardwares. This rendering method improves the rendering speed by simplifying the determination of the pixel value of an intermediate depth image and applying newly developed normal vector calculation method. Moreover, we describe the 3D boundary encoding that reduces the involved data considerably without the penalty of image quality. The interactive speed of the binary rendering and the storage efficiency of 3D boundary encoding will accelerate the development of the PC-based human atlas.