We investigate the ion beam damage of clean Au (001) single crystals prepared under standard surface science techniques using sputter - anneal cycles. Under initial ion milling conditions using 4 keV Xe ions a significant amount of Xe was implanted into the bulk of the crystal. After a short period of time a Xe super structure developed which yielded 12 Å moire fringes under bright field imaging conditions. With a short anneal the implanted Xe concentration was reduced to the detection limit of Parallel Electron Energy Loss Spectroscopy (PEELS). With extended annealing, the bulk point defect concentration slowly decayed, independent of the surface reconstruction.