A method for fabricating a stacked semiconductor system with encapsulated through wire interconnects includes providing a substrate having a first side, a second side and a substrate contact; forming a via in the substrate contact and the substrate to the second side; placing a wire in the via; forming a first contact on the wire proximate to the first side and a second contact on the wire proximate to the second side; and forming a polymer layer on the first side leaving the first contact exposed. The method also includes stacking two or more substrates and electrically connecting the through wire interconnects on the substrates.