The present invention relates to systems and methods for preparing the trochlear groove of a patient's femur to receive a prosthesis thereon. In the system, a combination drill-and-alignment guide includes at least a proximal and intermediate section, and preferably also includes a distal section. Guide holes for receiving guide pins therein are located in the proximal and distal sections of the guide. After the guide is positioned using at least one of several visual and/or tactile guide references in the system, the guides pins are placed through the guide holes of the guide and into bone. The guide may then be removed and replaced by cannulated reamers that are rotated and used to resect a predetermined amount of bone around the guide pins. A prosthesis having at least a portion of an outer surface that substantially matches the trochlear groove of the patient in a pre-degenerated state is then implanted on the resected bone.