With a two-dimensional (2D) optical mask at lambda=1083 nm, nanoscale patterns are created for the first time in an atom lithography process using metastable helium atoms. The internal energy of the atoms is used to locally damage a hydrophobic resist layer, which is removed in a wet etching process. Experiments have been performed with several polarizations for the optical mask, resulting in different intensity patterns, and corresponding nanoscale structures. The results for a linear polarized light field show an array of holes with a diameter of 260 nm, in agreement with a computed pattern. With a circularly polarized light field a line pattern is observed with a spacing of lambdaroot2=766 nm. Simulations taking into account many possible experimental imperfections can not explain this pattern.