Today’s Minimally Invasive Surgery (MIS) is performed by inserting an endoscope along with long stem surgical tools into the incision holes in the patient’s body to capture real-time images. Although MIS has many advantages compared to an open surgery, it also introduces a number of constraints for surgeons. In this thesis, we propose a novel paradigm for surgeon computer interface which allows surgeons to use tracked surgical tools like a 3D input device to obtain more information regarding patients’ anatomy during the MIS. We offer using tracked surgical tools to extract the boundaries of an organ from cluttered specular surfaces in MIS. Through real-time image analysis of the state and gesture of surgical tools, we also propose three augmented systems to access patient’s pre-operative scans during the MIS.