Bone deformities are often complex three-dimensional (3D) deformities, and correcting them is difficult. To correct persistent clubfoot deformity in adolescents or adults, an external fixator is sometimes used to encourage tissue growth and preserve healthy tissues. However, it is difficult to set up, resulting in long surgeries and steep learning curves for surgeons. It is also bulky and obstructs patient mobility. In this paper, we introduce a new approach of defining clubfoot deformity correction as a six degrees-of-freedom (6DOF) correction, and then reducing it to just two degrees-of-freedom (2DOF) using the axis-angle representation. Therefore, only two physical trajectory joints are needed, which in turn enables a more compact fixator design. A computer planner was developed to minimize the bulk of the external fixator, and to optimize the distraction schedule to avoid overstretching the soft tissues. This reduces the learning curve for surgeons and shortens surgery time. To validate the system, a patient-specific clubfoot simulator was developed, and four experiments were performed on the clubfoot simulator. The accuracy of midfoot correction was 11 mm and 3.5 deg without loading, and 41 mm and 11.7 deg with loading. While the external fixator has to be more rigid to overcome resistance against correction, the surgical system itself was able to achieve accurate correction in less than 2 h. This is an improvement from the current method, which takes 2.5–4.5 h.