In a MEMS device, an oxide layer is disposed between first and second semiconductor layers and MEMS resonator is formed within a cavity in the first semiconductor layer. A first electrically conductive feature functionally coupled to the MEMS resonator is exposed at a surface of the first semiconductor layer, and an insulating region is exposed at the surface of the first semiconductor layer adjacent the first electrically conductive feature. A semiconductor cover layer is bonded to the surface of the first semiconductor layer to hermetically seal the MEMS resonator within the cavity. A second electrically conductive feature extends through the semiconductor cover layer to contact the first electrically conductive feature, and an isolation trench extends through the semiconductor cover layer to the insulating region to electrically isolate a conductive path formed by the first and second electrically conductive features.