Mask based pattern generation is a crucial step in microchip production. The next generation Extreme Ultra Violet (EUV) lithography instruments with a wavelength of \SI{13.5}{\nano\meter} is currently under development. In principle this allows patterning down to a few \si{\nano\meter} resolution in a single exposure. However, there are many technical challenges due to the very high energy of the photons among others. Lithography with metastable atoms has been suggested as a cost effective, less complex alternative to EUV lithography. The big advantage of atom lithography is that the kinetic energy of an atom is much smaller than that of a photon for a given wavelength. However up till now no method has been available for making masks for atom lithography that can produce arbitrary, high resolution patterns. Here we present a solution to this problem. First, traditional binary holography is extended to near-field binary holography, based on Fresnel diffraction. By this technique, it is demonstrate that it is possible to make masks that can generate arbitrary patterns in a plane in the near-field (from the mask) with a resolution down to a few \si{\nano\meter} using a state of the art metastable helium source. We compare the flux of this source to that of an established EUV source (ASML, NXE:3100) and show that patterns can potentially be produced at comparable speeds. Finally we present an extension of the grid based holography method for a grid of hexagonally shaped subcells. Our method can be used with any beam that can be modeled as a scalar wave, including other matter wave beams such as helium ions, electrons or acoustic waves.