Creating a personalized implant for cranioplasty can be costly and aesthetically challenging, particularly for comminuted fractures that affect a wide area. Despite significant advances in deep learning techniques for 2D image completion, generating a 3D shape inpainting remains challenging due to the higher dimensionality and computational demands for 3D skull models. Here, we present a practical deep-learning approach to generate implant geometry from defective 3D skull models created from CT scans. Our proposed 3D reconstruction system comprises two neural networks that produce high-quality implant models suitable for clinical use while reducing training time. The first network repairs low-resolution defective models, while the second network enhances the volumetric resolution of the repaired model. We have tested our method in simulations and real-life surgical practices, producing implants that fit naturally and precisely match defect boundaries, particularly for skull defects above the Frankfort horizontal plane.