Method and apparatus for implanting radially expandable prostheses in the body lumens rely on tacking or anchoring of the prostheses with separately introduced fasteners. The prostheses may be self-expanding or balloon expandable. After initial placement, a fastener applier system is introduced within the expanded prostheses to deploy a plurality of fasteners at least one prosthesis end, usually as each end of the prosthesis. The fasteners are usually helical fasteners which are delivered from a helical track in the fastener applier by rotation with a rotator wire. The fasteners will be applied singly, typically in circumferentially spaced-apart patterns about the interior of each end of the prosthesis.