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Nanohole tetragonal and trigonal arrays as well as Al dot tetragonal and hexagonal arrays were successfully formed on Si substrates by the use of AFM nano-indentation and anodic oxidation. The ordered array of nanoholes could be obtained only at an indenting interval that depended on the anodic voltage. An Al dot hexagonal array with the nearest neighbor distance of 34 nm was formed. For further shrinkage of the Al dots, reduction of the indenting interval at an adequate anodic voltage would be necessary.