Disclosed herein is an easy and well-integrated method of etching features to different depths in a crystalline substrate, such as a single-crystal silicon substrate. The method utilizes a specialized masking process and takes advantage of a highly selective etch process. The method provides a system of interconnected, variable depth reservoirs and channels. The plasma used to etch the channels may be designed to provide a sidewall roughness of about 200 nm or less. The resulting structure can be used in various MEMS applications, including biomedical MEMS and MEMS for semiconductor applications.