Minimally invasive surgery in orthopedic field is considered to be a challenging problem with a milling robot. One objective of this study is to minimize collision of the cutting tool with soft tissue. The authors have developed a robot with redundant axis to avoid the collision so far. Some important components are modeled based on physical requirements, and a geometric optimization approach based on the model has been also proposed to improve performance. In this paper, a protective mechanism to cover the non-working part of the cutting edge is proposed to avoid soft tissue damage. Hardware and software have been developed for this application and the effectiveness of this technique was evaluated with urethane bone.