Three-dimensional porous alumina microstructures with vertically aligned nanopore array were self-assembled by anodic oxidation followed by an etching with phosphoric acid. By introducing micro-scaled hollow patterns to the initial aluminum surface by micro-contact imprinting, ordered microstructure arrays could be fabricated in large areas. Origin for the different etching rates of porous alumina membrane is believed to be the structural non-uniformity of the nanopore membranes: the porous alumina around the hollow areas introduced by the imprinting is stable against chemical etching due to the bent nanopores formed on the sidewall of the hollows. We can fabricate various porous alumina microstructure arrays in required positions by using this method and the shapes of the microstructures can be modified by regulating the applied voltage and selecting the intervals for the hollow areas. The present technique has a merit that three-dimensional building blocks with built-in nanopores can be fabricated whereas the conventional porous alumina has been a two-dimensional membrane. (C) 2012 The Electrochemical Society. [DOI: 10.1149/2.038204jes] All rights reserved.