A substrate of thin micromagnets covered by a template of microwells is used to direct the assembly of superparamagnetic colloidal beads into two-dimensional arrays. It is confirmed that the magnetization of the micromagnets can direct beads to programmed locations on the substrate with assistance of externally applied magnetic fields. Empirical investigations on this topic were guided by mathematical models with the intent to elucidate the conditions that promote a single bead to be assembled in the desired microwells. To demonstrate that this technique is programmable, heterogeneous arrays of colored beads are produced.