Energetic neutral atom beam lithography/epitaxy (ENABLE) is a versatile technique recently developed for patterning nanoscale features into polymer substrates. ENABLE achieves the direct activation of surface chemical reactions by exposing substrates to a beam of energetic neutral atoms. Polymers that form volatile oxidation products may be anisotropically etched using a neutral beam of oxygen atoms at rates exceeding 100 nm/min, avoiding problems associated with charged species inherent to other etching techniques. We report on a top-down approach for producing high-aspect-ratio nanoscale structures in polymeric materials using ENABLE. Masking techniques suitable for ENABLE etching are discussed along with applications involving the rapid production of nanoscale features over large areas.