A semiconductor device has a semiconductor die. The semiconductor die is disposed over a conductive substrate. An encapsulant is deposited over the semiconductor die. A first interconnect structure is formed over the encapsulant. An opening is formed through the substrate to isolate a portion of the substrate electrically connected to the first interconnect structure. A bump is formed over the first interconnect structure. Conductive vias are formed through the encapsulant and electrically connected to the portion of the substrate. A plurality of bumps is formed over the semiconductor die. A first conductive layer is formed over the encapsulant. A first insulating layer is formed over the first conductive layer. A second conductive layer is formed over the first insulating layer and first conductive layer. A second insulating layer is formed over the first insulating layer and second conductive layer. Protrusions extend above the substrate.