To improve the safety, accuracy and effectiveness of surgery, while also reducing surgical trauma, three-dimensional spatial positioning of the surgical instruments can be achieved through the accuracy of integration of medical imaging to guide their operation during surgery. Therefore, prior to surgery, registration is required to establish the relationship between the actual positioning of the surgical instruments and their imaged position. The accuracy of such registration directly determines the precision of navigation. Taking into account the shortcomings and deficiencies of the current fiducial marker registration methods, this paper proposes an automatic fiducial marker extraction and matching algorithm. In order to facilitate automatic recognition and extraction of the fiducial markers the authors of this paper designed fiducial marker with CT values and shapes that provide recognizable characteristics which help to meet the demands of the positioning requirements. The extraction of such fiducial markers can be easily automated, significantly reducing the difficulty in developing an extraction algorithm. After fiducial marker extraction the registration algorithm and the Iterative Closest Point (ICP) algorithm can be combined to achieve matching between the fiducial marker and point set model of the fiducial marker. According to the matching results indicating the positional relationship between the each fiducial marker and its retroreflective sphere, the center coordinate of the retroreflective sphere in the image can be acquired, hence providing an easy way to undertake registration of the different spatial representations of the patient.