An apparatus for an ion trap includes an electrically conductive substrate having top and bottom surfaces and having vias that cross from the top surface to the bottom surface. The apparatus includes a pair of planar first electrodes supported over said top surface and second electrodes having planar surfaces. The planar surfaces are located over said top surface, and portions of the planar surfaces are located laterally adjacent to said planar first electrodes. One of the second electrodes includes a portion that is located in one of the vias and traverses the substrate.