A method of the present invention is presented for deep etching of features on a surface. In one embodiment, the method includes providing a substrate having a surface selected to undergo a feature etching process and coating the substrate surface with a protective layer and an imprintable layer. The coated substrate is then subjected to a feature imprinting and etching process. Subsequent to the feature etching process, exposed portions of the protective layer are removed, exposing a well-defined, topographically patterned substrate. In addition, an apparatus for undergoing a feature etching process is disclosed. The apparatus comprises a substrate, an imprintable layer selected to undergo an imprinting process, and a protective layer positioned between the substrate and the imprintable layer. The protective layer may be selected to provide additional protection to selected portions of the substrate and to prevent non-planar byproducts of the feature etching process from transferring to the selected portions.