Nanotechnology creates a new challenge for materials characterization because device properties now depend on size and shape as much as they depend on the traditional parameters of structure and composition. Here we show that Z-contrast tomography in the scanning transmission electron microscope has been developed to determine the complete three-dimensional size and shape of embedded structures with a resolution of approximately 1 cubic nanometer. The results from a tin/silicon quantum dot system show that the positions of the quantum dots and their size, shape, structure, and formation mechanism can be determined directly. These methods are applicable to any system, providing a unique and versatile three-dimensional visualization tool.