An ion beam assisted method for large-area fabrication of nanodot arrays in anodic alumina oxide (AAO) templates was investigated. By this method, ordered arrays of Ni and Au nanodots with highly uniform diameters and density of 1.2×1010/cm2 were fabricated. The diameter and packing density of nanodots can be controlled by the cell parameters of AAO template. The fabrication method presented here can be extended to many other materials and allows further investigation of the size related characteristics in nanodot structures.