Custom medical treatment is being widely adapted to lots of medical applications. A technology for 3D modeling is strongly required to fabricate medical implants for individual patient. Needs on true 3D CAD data of a patient is strongly required for tissue engineering and human body simulations. Medical imaging devices show human inner section and 3D volume rendering images of human organs. CT or MRI is one of the popular imaging devices for that use. However, those image data is not sufficient to use for medical fabrication or simulation. This paper mainly deals how to generate 3D geometry data from those medical images. A new image processing technology is introduced to reconstruct 3D geometry of a human body vacancy from the medical images. Then a surface geometry data is reconstructed by using Marching cube algorithm. Resulting CAD data is a custom 3D geometry data of human vacancy. This paper introduces a novel 3D reconstruction process and shows some typical examples with implemented software.