A method of manufacturing a three-dimensional semiconductor device includes forming a bi-layer sacrificial stack on a top wafer and a bottom wafer each including a series of interconnects in a dielectric substrate. The bi-layer sacrificial stack includes a second sacrificial layer on a first sacrificial layer. The method also includes selectively etching the second sacrificial layers to form a first pattern of projections on the top wafer and a second pattern of projections on the bottom wafer. The first pattern of projections is configured to mesh with the second pattern of projections. The method also includes positioning the top wafer on the bottom wafer and releasing the top wafer such that engagement between the first pattern of projections and the second pattern of projections self-aligns the plurality of interconnects of the top wafer with the plurality of interconnects of the bottom wafer within a misalignment error.