A flexible "scaffold" envelope is disclosed which can be used to replace damaged cartilage in knees, shoulders, or other joints of a mammalian body. Designed for use in arthroscopic surgery, the envelope is sufficiently flexible to allow it to be rolled up or folded and inserted into a knee or other joint via a small skin incision. Before insertion, a segment of damaged cartilage is removed from a bone surface, and the bone surface is prepared, using various tools and alignment guides disclosed herein. After the envelope is inserted into the joint, it is unfolded, positioned properly, and anchored and cemented to a bone surface. After anchoring, the envelope is filled via an inlet tube with a polymeric substance that will set and solidify at body temperature. During filling and setting, the surgeon can manipulate the exterior shape of the scaffold envelope, to ensure that the implant will have a proper final shape after the polymer has cured into fully solidified form. Using these materials and methods, a synthetic replacement can be created for damaged or diseased cartilage, having a smooth surface and a non-rigid stiffness closely resembling natural cartilage. The entire procedure can use minimally invasive tools and methods, to avoid having to cut open and fully expose a joint that is being repaired. Various devices and methods are disclosed to facilitate this procedure, including tools and devices to help ensure proper arthroscopic preparation of large bone surfaces, and proper positioning, alignment, anchoring, and filling of a scaffold envelope.