Colloidal aggregates with well-controlled sizes, shapes, and structures have been fabricated by dewetting aqueous dispersions of monodispersed spherical colloids across surfaces patterned with two-dimensional arrays of relief structures (or templates). The capability and feasibility of this approach have been demonstrated with the organization of polymer latex or silica beads into homo-aggregates, including circular rings; polygonal and polyhedral clusters; and linear, zigzag, and spiral chains. It was also possible to generate hetero-aggregates in the configuration of HF and H2O molecules that contained spherical colloids of different sizes, compositions, densities, functions, or a combination of these features. These uniform, well-defined aggregates of spherical colloids are ideal model systems to investigate the aerodynamic, hydrodynamic, and optical properties of colloidal particles characterized by non-spherical shapes and/or complex topologies. They can also serve as a new class of building blocks to generate hierarchically self-assembled structures that are expected to exhibit interesting features valuable to areas ranging from condensed matter physics to photonics.