Selective dorsal rhizotomy (SDR) is a difficult, risky, and sophisticated operation, in which a laminectomy should not only expose an adequate surgical field of view but also protect the patient’s spinal nerves from injury. Digital models play an important role in the pre-and intra-operation of SDR, because they can not only make doctors more familiar with the anatomical structure of the surgical site, but also provide precise surgical navigation coordinates for the manipulator. This study aims to create a 3D digital model of a patient-specific lumbar vertebra that can be used for planning, surgical navigation, and training of the SDR operation. The 3D printing model is also manufactured for more effective work during these processes. Traditional orthopedic digital models rely almost entirely on computed tomography (CT) data, which is less sensitive to soft tissues. Fusion of the bone structure from CT and the neural structure from magnetic resonance imaging (MRI) is the key element for the model reconstruction in this study. The patient’s specific 3D digital model is reconstructed for the real appearance of the surgical area and shows the accurate measurement of inter-structural distances and regional segmentation, which can effectively help in the preoperative planning and training of SDR. The transparent bone structure material of the 3D-printed model allows surgeons to clearly distinguish the relative relationship between the spinal nerve and the vertebral plate of the operated segment, enhancing their anatomical understanding and spatial sense of the structure. The advantages of the individualized 3D digital model and its accurate relationship between spinal nerve and bone structures make this method a good choice for preoperative planning of SDR surgery.