An arbitrary gap between the two chips of a MEMS device arranged in a flip-chip arrangement is achieved by etching into a first substrate to form mesas which act as spacers between which, or even on which, any required circuit elements are formed. Points of a layer at a first surface of the second substrate within which MEMS structures are made are bonded to the mesas of the first substrate. The second substrate is then removed, leaving the structures bonded to the mesas. The mesas may be formed by placing a hard mask, such as silicon oxide, which defines the desired pattern of mesas on the first substrate, and then etching the unmasked portion of the substrate using a mixture of potassium hydroxide (KOH) with isopropanol (IPA) or, tetramethyl ammonium hydroxide (TMAH) mixed with a surfactant, e.g., nonylphenol ethoxy ether or other equivalent compounds.