Polymer- and surfactant-templated mesoporous inorganic materials offer a unique combination of controllable nanoscale architecture, materials variation and low-cost solution processing. Inorganic materials can be produced with a range of periodic pore structures, with feature size ranging from 2 to 30 nm, and from a diverse set of materials. Unfortunately in thin-film form, the pores of the ubiquitous hexagonal honeycomb phase tend to lie in the plane of the substrate making these materials unsuitable for applications where diffusion into the pores is required. Here, we show that nanometre-scale epitaxy on a patterned substrate can be used to form vertically oriented pores in honeycomb-structured films. We use the surface of cubic mesoporous films to form the pattern; as such, our method does not sacrifice the simple processing advantages of a self-assembled system. A precise lattice match between the hexagonal and cubic films is needed for vertical orientation, a condition that can be achieved using mixed templates or selective pore swelling. Pore orientation is characterized by a combination of microscopy and diffraction. Here, we present alignment data on oriented nanopores in the 10-15 nm range, but the method should be applicable across the 2-30 nm pore size range of these self-organized materials.