In this paper we present pulse deposition as a new method to favor the self-assembly of nanostructured materials. Nucleation and growth of gold thin layers deposited on highly oriented pyrolytic graphite substrate have been studied using scanning tunneling microscopy in air. Depositions were performed in a pulsed regime and, for comparison, continuously in time. Much higher cluster density and better arrangement of clusters are obtained for pulse deposition than for gold deposited continuously. The formation of the channel structure of the deposited layer is favored and achieved earlier. The results indicate that the number of surface defect sites increases with subsequent pulses, behavior attributed to the previously formed clusters taking on the role of surface defect sites.