Periodic, highly uniform arrays of dome-like Ge quantum dots (QDs) with 50 nm interdot pitch have been achieved on Si (001). The Si surface was patterned using ultra-low-dose focused ion beam and defect-selective etching, resulting in a continuously height-modulated, "egg-carton" morphology. The directed self-assembly process is robust, occurring across a range of ion doses, growth temperatures, and deposition rates. By selectively etching off the Ge dots to reveal the underlying Si surface just prior to Ge growth, we showed that Ge QDs preferentially formed on crowns (regions of negative curvature) rather than pits (regions of positive curvature) as is mostly seen in the literature. The width of the QD size distribution mimics that of the underlying substrate pattern, indicative of a complete lack of coarsening during the Ge growth, despite the small length scales, and extensive mass transport leading to QD formation.