Fast, large area patterning of arbitrary structures down to the nanometre scale is of great interest for a range of applications including the semiconductor industry, quantum electronics, nanophotonics and others. It was recently proposed that nanometre-resolution mask lithography can be realised by sending metastable helium atoms through a binary holography mask consisting of a pattern of holes. However, these first calculations were done using a simple scalar wave approach, which did not consider the dispersion force interaction between the atoms and the mask material. To access the true potential of the idea, it is necessary to access how this interaction affects the atoms. Here we present a theoretical study of the dispersion force interaction between an atom and a dielectric membrane with a hole. We look at metastable and ground state helium, using experimentally realistic wavelengths (0.05–1 nm) and membrane thicknesses (5–50 nm). We find that the effective hole radius is reduced by around 1–7 nm for metastable helium and 0.5–3.5 nm for ground-state helium. As expected, the reduction is largest for thick membranes and slow atoms.