A method for preparing at least a first bone for receiving a prosthesis can include positioning an IM member in a bone. A scaffold, skeleton or frame can be located onto the bone at a desired location. An alignment assembly can be coupled to the frame. The alignment assembly can be moved relative to the IM member to position the frame at a desired location relative to the bone. The frame can be fixed to the bone at the desired location. A cavity can be reamed into the bone using at least a portion of the alignment assembly as a guide. The alignment assembly can be removed from the frame. A cutting block can be coupled to the first attachment portion. Cuts can be prepared in the bone using the cutting block as a guide.