Germanium nucleation on a silicon surface typically proceeds via spontaneous formation of nanoscopic islands, or quantum dots (QDs), at random locations. However, potential applications of epitaxial QDs, such as quantum cellular automata, require precise control of Ge island positions on Si in clusters with the individual islands' separation of tens of nanometers or less. Controlled Ge island placement with an inter-island separation down to 100 nm can be reliably obtained by depositing Ge onto a Si(001) surface modified with a low dose focused ion beam (FIB) pattern to create preferred nucleation sites for individual islands. Here we investigate QD self-assembly of multiple islands on single topographical features intended to obtain clusters of QDs with smaller separations. We observe formation of 50 nm clusters on a single location defined by the FIB patterning of a larger and shallower feature, where cluster formation is promoted by reduced surface diffusion. We also discuss cluster formation on single sites defined by residual trenches on a footprint of a larger island that has been desorbed. We propose that controlled placement of islands during the first deposition may result in greater control over subsequent cluster size and placement fidelity due to improved uniformity of target features. © 2014 World Scientific Publishing Company.