We successfully fabricated a square pattern of anodic alumina oxide (MO) template in thin Al film grown on Si substrate utilizing focused ion beam (FIB) milled indent. The pore size and its period of the square matrix were about 50 nm and 100 nm, respectively. We found that the minimum indented depth is required to satisfy the critical electric field which is a vertical component toward downward. In addition, we found that the anodizing voltage plays an important role in determining the pore shape and uniformity. The higher anodizing voltage not only reduces the minimum indent depth that is required to create a matrix array but also improves the uniformity of pore shapes in the matrix array. (C) 2009 Elsevier B.V. All rights reserved.