Nanoporous anodic aluminum oxide (AAO) has been used widely as a template for device fabrication. In many nanostructured electro-optical device designs, AAO grown on an ITO substrate is the desired configuration. However, a residual thin aluminum oxide barrier layer between ITO and the AAO pores remains and process non-uniformities during the template fabrication can cause serious problems in the quality of nanowires deposited later in these pores. It was observed that in many templates, even the pores closest to each other could have their barrier layer thicknesses differ by as much as 10-20 nm. In this paper, causes and remedies for this non-uniformity are investigated, including the effects of a thin Ti interlayer inserted between the ITO and AAO. Templates with different Ti layer thickness and annealing conditions were compared. Mechanisms for the formation of voids beneath the barrier layer were analyzed and studied experimentally. Reactive ion etch (RIE) was found to be the preferred method to mitigate process non-uniformities. Using the above methods, barrier-free AAO templates on ITO substrates were obtained; their thicknesses ranged from 200 to 1000 nm. The characteristics of CdS nanowires electrodeposited into the initial templates with non-uniform barrier layer thicknesses and into the processed, barrier-free templates were compared.