Three-dimensional structures are provided which improve manufacturing yield for certain structures in semiconductor devices. The three-dimensional structures take into account the interaction between an upper layer and a lower layer where the lower layer has a tendency to form a non-planar surface due to its design. Accordingly, structures built on a layer above the lower layer are formed on a more planar surface and thus are more likely to function properly. The changes to improve manufacturing yield are made at the design stage rather than at the fabrication stage.