The introduction of voids in a magnetic thin-film alters the stray field distribution and enables the tailoring of the corresponding physical properties. Here we present a detailed study on thin magnetic nanohole arrays (NhAs) grown on top of hexagonally-ordered anodic aluminum oxide (AAO) substrates. We address the effect of AAO topography on the corresponding electrical and magneto-transport properties. Optimization of the AAO topography led to NhAs with improved resistance and magnetoresistance responses, while retaining their most important feature of enhanced coercivity. This opens new pathways for the growth of more complex structures on AAO substrates, a crucial aspect for their technological viability.