A micro-electrical-mechanical system (MEMS) resonator device includes a top side electrode overlaid with an interface layer including a material having a surface (e.g., gold or other noble metal, or a hydroxylated oxide) that may be functionalized with a functionalization (e.g., specific binding or non-specific binding) material. The interface layer and/or an overlying blocking material layer are precisely patterned to control locations of the interface layer available to receive a self-assembled monolayer (SAM), thereby addressing issues of misalignment and oversizing of a functionalization zone that would arise by relying solely on microarray spotting. Atomic layer deposition may be used for deposition of the interface layer and/or an optional hermeticity layer. Sensors and microfluidic devices incorporating MEMS resonator devices are also provided.