In this work, it has been shown that, through a highly controlled process, the chemical etching of the anodic aluminum oxide membrane barrier layer can be performed in such a way as to achieve nanometer-scale control of the pore opening. As the barrier layer is etched away, subtle differences revealed through AFM phase imaging in the alumina composition in the barrier layer give rise to a unique pattern of hexagonal walls surrounding each of the barrier layer domes. These nanostructures observed in both topography and phase images can be understood as differences in the oxalate anion contaminated alumina versus pure alumina. This information bears significant implication for catalysis, template synthesis, and chemical sensing applications. From the pore opening etching studies, the etching rate of the barrier layer (1.3 nm/min) is higher than that of the inner cell wall (0.93 nm/min), both of which are higher than the etching rate of pure alumina layer (0.5-0.17 nm/min). The established etching rates together with the etching temperature allow one to control the pore diameter systematically from 10 to 95 nm.