System-in packages, or multichip modules, are described which can include multi-layer chips and multi-layer dummy substrates over a carrier, multiple through vias blindly or completely through the multi-layer chips and completely through the multi-layer dummy substrates, multiple metal plugs in the through vias, and multiple metal interconnects, connected to the metal plugs, between the multi-layer chips. The multi-layer chips can be connected to each other or to an external circuit or structure, such as mother board, ball grid array (BGA) substrate, printed circuit board, metal substrate, glass substrate, or ceramic substrate, through the metal plugs and the metal interconnects.