Structure and method for fabricating a barrier layer that separates an electromechanical device and a CMOS device on a substrate. An example structure includes a protective layer encapsulating the electromechanical device, where the barrier layer may withstand an etch process capable of removing the protective layer, but not the barrier layer. The substrate may be silicon-on-insulator or a multilayer wafer substrate. The electromechanical device may be a microelectromechanical system (MEMS) or a nanoelectromechanical system (NEMS).