We established a method to clean the Si surface that exists at the bottom of anodic aluminum oxide (AAO) nanoholes after removal of the amorphous barrier layer, and we succeeded in the preparation of epitaxial Cu dot arrays on the Si surface in the nanoholes. The Si surfaces at the AAO nanohole bottoms were cleaned with dilute hydrofluoric acid after annealing at 900 degrees C in Ar ambient, and we sputtered Cu on the AAO template to form Cu dot arrays. This method for preparing nanohole arrays on a single crystalline substrate enables growth of a variety of highly regular epitaxial nanodot/wire arrays. (c) 2006 The Electrochemical Society.