Self-assembled cobalt particle arrays are formed by annealing, which cause agglomeration (dewetting) of thin Co films on oxidized silicon substrates that are topographically prepatterned with an array of 200-nm-period pits. The Co nanoparticle size and uniformity are related to the initial film thickness, annealing temperature, and template geometry. One particle per 200-nm-period pit is formed from a 15-nm film annealed at 850 degrees C; on a smooth substrate, the same annealing process forms particles with an average interparticle distance of 200 nm. Laser annealing enables templated dewetting of 5-nm-thick films to give one particle per pit. Although the as-deposited films exhibit a mixture of hexagonal close-packed and face-centered cubic (fcc) phases, the ordered cobalt particles are predominantly twinned fcc crystals with weak magnetic anisotropy. Templated dewetting is shown to provide a method for forming arrays of nanoparticles with well-controlled sizes and positions.