Sri clustering on Si(111) samples was studied during deposition at 100 degreesC and after an additional postdeposition anneal at 200 degreesC for 5 min. These conditions lead to early stage morphologies for the surface phase separation process of the thin film. We focus in this atomic force microscopy study on (i) the evolution of the partial ordering in the nearest-neighbor distance distributions observed in the late stage of phase separation and (ii) on the role of well-defined substrate defects on the development of the early stage morphology.