Atom lithography uses standing wave light fields as arrays of lenses to focus neutral atom beams into line patterns on a substrate. Laser cooled atom beams are commonly used, but an atom beam source with a small opening placed at a large distance from a substrate creates atom beams which are locally geometrically collimated on the substrate. These beams have local offset angles with respect to the substrate. We show that this affects the height, width, shape, and position of the created structures. We find that simulated effects are partially obscured in experiments by substrate-dependent diffusion of atoms, while scattering and interference just above the substrate limit the quality of the standing wave lens. We find that in atom lithograp...