It is well documented that buried layers in quantum dot (QD) superlattices influence the position of quantum dots in the subsequently grown layers through strain field interactions (e.g.1,2, 3,4). Using the Focused Ion Beam (FIB) tomographic technique we have reconstructed the 3D relationship of successive layers of coherent Ge QDs separated by epitaxial Si capping layers - a “QD superlattice”.Techniques such as Atomic Force Microscopy (AFM) and Scanning Tunneling Microscopy (STM) can only look at a single surface layer of QDs or, in the case of Transmission Electron Microscopy (TEM), look at a two-dimensional projection of a three-dimensional volume so that 3D relationships need to be inferred. Since the strain interactions are complex, an enhanced fundamental understanding of these self-organization mechanisms can more directly be obtained from full 3D reconstructions of these structures.By capping with Si at 300°C we were able to grow QD superlattices with QDs tens of nanometers in height. This places them within the resolution of the FIB tomographic technique to reconstruct. Using the FIB we performed in-situ serial sectioning of the QD superlattice and then reconstructed the QD superlattice. The reconstruction was then analyzed to investigate the ordering of the QDs.Results from a reconstruction of a superlattice matrix will be presented with analysis of the self-ordering of the QDs. Observations of a novel self-limiting (in height) morphology, the quantum mesa, associated with the capping technique used will also be discussed.