A patient-specific cutting guide system comprises at least two instruments. One is a positioner configured to locate a fiducial marker on a patient's bone and to be secured in three axes. The second is a cutting guide that cooperates with the positioner and delineates cuts to be made. The instruments are designed from images of the bone with the marker already in place. Preferably, a positioner comprises at least three targeting apertures configured to locate at least three non-linear markers. The cutting guide comprises top surface contours that guide the depth of the cuts. A method of forming this system comprises placing at least one marker (preferably three) on a patient's bone, then imaging the bone, forming a positioner designed to incorporate the marker position, and forming a cutting guide configured to be oriented and anchored by the positioner.
