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This work presents a new technique for surface patterning with focused ion beams. The technique is based on chemical decomposition in the bulk of a polymer substrate with negligible surface sputtering effects. By using a focused helium ion beam, generated in a helium ion microscope, we show that the surface height of polymethyl methacrylate substrates can be patterned with nanometer depth precision, while preserving the essential features of the nanostructures prefabricated on this surface. The key factors that control this patterning process are discussed.