Structures and methods of fabricating semiconductor wafer assemblies that encapsulate one or die in a cavity etched into an oxide bonded semiconductor wafer stack. The methods generally include the steps of positioning the die in the cavity, mechanically and electrically mounting the die to the wafer stack, and encapsulating the die within the cavity by bonding a lid wafer to the wafer stack in one of multiple ways. Semiconductor processing steps are applied to construct the assemblies (e.g., deposition, annealing, chemical and mechanical polishing, etching, etc.) and connecting the die (e.g., bump bonding, wire interconnecting, ultrasonic bonding, oxide bonding, etc.) according to the embodiments described above.