In aortic vascular surgery, a navigation system must represent the anatomical map of individual patient in order to detect the important artery. To provide a proper fit for positions along the dorsoventral axis, the spinous process was added to a currently used anatomical point set consisting of four anterior body landmarks. In addition, we attempted to reduce the registration error by compensating for alignment errors resulting from variations in tissue thickness at each landmark. The alignment values were examined using a human phantom consisting of a skeleton model with subcutaneous tissue in the semilateral position. Using this method, a phantom simulation and five clinical trials were performed. Target errors were evaluated at the orifice of the intercostal artery. In the phantom simulation, the error at the target point was 4.1 ± 2.7 mm. However, for one patient undergoing thoracoabdominal aortic aneurysm replacement surgery, the target error was 8.0 mm using the proposed method.