We investigate the formation of an ordered array of metal nanoclusters via selective doping of microphase-separated nanodomains in thin diblock copolymer films. Nanostructure formation during this doping process is probed in situ with microbeam grazing incidence small-angle X-ray scattering (mu GISAXS) and ex-situ with atomic force microscopy (AFM). During sputter deposition of iron on the thin film template of polystyrene-block-poly(methyl methacrylate) P(S-b-MMA) copolymer, having upright cylindrical domains of PMMA, iron atoms selectively dope the PMMA domains due to the preferential chemical affinity. AFM confirms the mu GISAXS results that the iron atoms preferentially wet the PMMA domains at low amount of sputter deposited iron. Up to a threshold of a nominal thickness of 2.0 rim deposited iron, the atoms wet only the PM:MA domains and create the ordered array of metal nanoclusters. Above this threshold thickness the iron nanostructures grow laterally and finally cover the complete template surface.