In an example, a chip-scale atomic clock physics package is provided. The physics package includes a body defining a cavity having a base surface and one or more side walls. The cavity includes a first step surface and a second step surface defined in the one or more side walls. A first scaffold mounted to the base surface in the cavity. One or more spacers defining an aperture therethrough are mounted to the second step surface in the cavity. A second scaffold is mounted to a first surface of the one or more spacers spans across the aperture of the one or more spacers. A third scaffold is mounted to a second surface of the one or more spacers in the cavity and spans across the aperture of the one or more spacers. Other components of the physics package are mounted to the first, second, and third scaffold.