Package assemblies for and methods of packaging integrated circuit chips are described. Disclosed package assemblies have spacers and recessed regions comprising IC chips. Architectural structures are provided that enable, for example, three dimensional (3D) packaging (or system in package (SiP) or multi-chip modules), systems-on-chip 3D packaging, and hybrid 3D bonding. Embodiments of the invention can be used, for example, to create logic-to-memory, memory-to-memory, and logic-to-logic interface stacking assemblies.