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Summary form only given.Using neutral atoms for lithography is a new method of generating nanostructures on a substrate. This method is based on light masks formed by interfering laser beams perpendicular to the atomic beam. One- and two-dimensional periodic structures have been fabricated by various groups using light masks with intensity gradients and uniform polarization. The resulting periods are half the laser wavelength or greater. Atoms with a magnetic substructure in the electronic ground state are strongly sensitive to light polarization and static magnetic fields. Our work presents a detailed investigation of possible two-dimensional light field configurations including polarization gradients and static magnetic fields. The resulting nanostructures obtained in an experimentally realistic situation are simulated.