Nanodevices require the elaboration of periodic arrays of nanoparticles with adjustable periodicities. In this way, "bottom-up" and "top-bottom" methods are currently developed. We focus on a "top-down/bottom-up" approach based on the direct deposition of nanoclusters on patterned graphite surfaces. In this case, artificial defects (created by Focused Ion Beam (FIB)) are expected to act as nucleation centers for the deposited clusters. Clusters are preformed in free phase from a laser vaporization source. Such clusters (gold and cobalt platinum clusters) are deposited in a soft landing route onto various substrates (free or patterned) at moderate temperature T < 600 K. This technique allows the preparation of nanogranular films keeping the memory of the free phase: the elementary grain just coincides with the preformed cluster. We focus on the effect of ion dose on the morphology of defects as well as the evolution of the cluster organization with artificial defect nature. Experimental arrangements are also compared with predictions derived from a kinetic Monte Carlo approach. This study underlines the high sensitivity of clusters to ultra small topographic defects. (c) 2004 Elsevier B.V. All rights reserved.