Ordered arrays of anodic alumina nanopores with uniform pore diameters have been fabricated by self-organized anodization of aluminum. However, gradient or alternating diameter nanopore arrays with designed interpore distances have not been possible. In this study, focused ion beam lithography is used to fabricate hexagonally arranged concaves with different diameters in designed arrangements on aluminum surfaces. The patterns are then used to guide the further growth of alumina nanopores in the subsequent oxalic acid anodization. Gradient and alternating nanopore arrangements have been attained by FIB patterning guided oxalic acid anodization. The fundamental understanding of the process is discussed.