In a spent fuel pool of a nuclear power plant, there is provided a system for aligning a nuclear fuel bundle and handling selected fuel rods within the fuel bundle. The bundle includes water rods, full-length and part-length fuel rods extending through a plurality of fuel spacers provided between top and bottom ends of the bundle, each spacer having a plurality of cells accommodating corresponding fuel and water rods. The system includes a bundle alignment system for aligning the fuel rods and water rods, a rod grapple tool to extract selected part-length rods from the bundle, and a fuel rod guide block slidable onto the top end of the bundle for protecting an uppermost fuel spacer of the bundle, and for aligning fuel rods within individual cells of all the fuel spacers in the fuel bundle.