A method of aligning a nuclear fuel bundle and handling selected fuel rods within the fuel bundle located in a spent fuel pool of a nuclear power plant. 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 method includes insertion of a rod grapple tool into a top end of a fuel bundle and down to a desired location within the bundle. A guide pin retrieval tool inserts into a side of the fuel bundle to remove a guide pin from a distal end of a gripper of the rod grapple tool, allowing the guide pin retrieval tool to grip a part-length fuel rod within the fuel bundle.