Anodic aluminum oxide (AAO) templates are emerging as a platform for simple, cost-effective, high-throughput top-down nanofabrication of regular arrays of nanostructures. Thus far, however, AAO pattern transfer has largely been restricted to smooth and chemically inert surfaces, mostly Silicon substrates. Here, we present a more generalizable strategy for preparing free-standing through-hole ultrathin alumina membranes (UTAMs) and transferring them to both smooth and rough substrates, thereby enabling the fabrication of centimeter-scale arrays of nanostructures with sub-100 nm feature diameters on almost arbitrary substrates. To validate the utility of our procedures, we transferred UTAMs to surfaces relevant for photocatalytic applications and prepared plasmonic photocathodes consisting of dense arrays of size-controlled sub-100 nm Au and Ni nanodots on top of chemically noninert NiOx thin films. To demonstrate the functionality of the fabricated structures, we used a plasmonic photocathode consisting of an array of sub-50 nm Au nanodots on NiOx/Al substrates to drive direct, plasmon-enhanced photoelectrocatalysis and found excellent device performance. We also successfully decorated very rough fluorine-doped tin oxide substrates with an array of high-density sub-100 nm nanodots. Our results extend the opportunities for AAO masks to serve as generic templates for novel applications that were previously prohibited by lack of methods to transfer to the required substrate.