Semiconductor Device and Method of Forming Hybrid Substrate with Uniform Thickness

A semiconductor device has a first hybrid substrate with a first thickness, and a second hybrid substrate with a second thickness different from the first thickness of the first hybrid substrate. An encapsulant is deposited around the first hybrid substrate and second hybrid substrate. A portion of the first hybrid substrate and a portion of the second hybrid substrate and a portion of the encapsulant can be removed after encapsulation to achieve uniform thickness for the first hybrid substate and second hybrid substrate. The first hybrid substrate has an embedded substrate, a first interconnect structure formed over a first surface of the embedded substrate, and a second interconnect structure formed over a second surface of the embedded substrate opposite the first surface of the embedded substrate. A plurality of conductive pillars is formed over the first interconnect structure. A plurality of conductive vias is formed through the embedded substrate.