In classical binary holography, a target pattern located at infinity is generated by the diffraction of a plane wave passing through a binary mask with holes of the same size, placed at specific positions of a rectangular grid. Fresnel binary atom holography was recently proposed as a means for achieving nanometer-resolution mask-based lithography with metastable atom beams. In practice, there will be fabrication imposed limits: the binary mask will have a minimum hole size, a minimum distance between the holes in the grid~(pitch), a maximum size, and the target pattern plane will always have a finite distance from the mask. In this paper, we show that, in praxis, for a given wavelength, mask, and target pattern sizes, there will be a cross-over value for the distance between the mask and the target pattern plane (the screen plane) which results in aliasing-free patterns. It is demonstrated how this insight can lead to the generation of better-resolved patterns of higher contrast and nanometer resolution can be achieved within experimental limitations. Since flux is one of the main factors influencing the quality of patterns fabricated by nano-lithography, we obtain an expression for the ``patterning flux'' (the flux that contributes to producing the target pattern, normalized by the flux that is incident onto the structured portion of the mask). Numerically we find that its ratio scales approximately like $x^{-2}$ where $x$ is the mask-screen distance over the cross-over distance. The method that we propose can be used with any beam that can be modeled as a scalar wave, including acoustic waves and other matter-wave beams such as helium ions or electrons.