We report a successful unification of standard lithographic approaches (top down), anisotropic etching of atomically smooth surfaces, and controlled crystallization of silicon quantum dots (bottom up) to produce silicon nanoclusters at desired locations. These results complement our previous demonstration of silicon nanocrystal uniformity in size, shape, and crystalline orientation in nanocrystalline silicon (nc-Si)/SiO2 superlattices, and could lead to practical applications of silicon nanocrystals in electronic devices. The goal of this study was to induce silicon nanocrystal nucleation at specific lateral sites in a continuous amorphous silicon (a-Si) film. Nearly all previous studies of silicon nanocrystals are based on films containing isolated nanocrystals with random lateral position and spacing. The ability to define precise two-dimensional arrays of quantum dots would allow each quantum dot to be contacted using standard photolithographic techniques, leading to practical device applications like high-density memories. In this work, a template substrate consisting of an array of pyramid-shaped holes in a (100) silicon wafer was formed using standard microfabrication techniques. The geometry of this substrate then influenced the crystallization of an a-Si/SiO2 superlattice that was deposited on it, resulting in preferential nucleation of silicon nanoclusters near the bottom of the pyramid holes. These clusters are clearly visible in transmission electron microscopy (TEM) images, while no clusters have been observed on the planar surface areas of the template. Possible explanations for this selective nucleation and future device structures will be discussed.