We have studied the effect of ion milling on the surface crystallinity of the metal oxide substratesLaAlO3,SrTiO3,andNdGaO3which are used for fabrication of high-TcJosephson junctions and circuits. Ion channeling of the milled substrates reveals a damage-induced peak corresponding to a disordered layer of≈60 Åat the surface. Annealing the substrates in oxygen ambient at various temperatures ranging from 600 to 1100 °C resulted in the regrowth of the damaged layer at the surface of the substrates as was indicated by the reduction in size of the surface peak observed in the channeled spectrum, as well as by formation of lattice steps as seen by atomic force microscopy. A significant reduction in the damage peak size and the formation of smooth completed lattice steps are seen only after annealing at temperatures⩾950 °C.©1997 American Institute of Physics.