Cobalt sputter deposition on a nanostructured polystyrene-block-poly(ethylene oxide), P(S-b-EO), template is followed in real time with grazing incidence small angle Xray scattering (GISAXS). The polymer template consists of highly oriented parallel crystalline poly(ethylene oxide) (PEO) domains that are sandwiched between two polystyrene (PS) domains. In situ GISAXS shows that cobalt atoms selectively decorate the PS domains of the microphase-separated polymer film and then aggregate to form surface metal nanopatterns. The polymer template is acting as a directing agent where cobalt metal nanowires are formed. At high metal load, the characteristic selectivity of the template is lost, and a uniform metal layer forms on the polymer surface. During the early stage of cobalt metal deposition, a highly asymmetric nanoparticles agglomeration is dominating structure formation. The cobalt nanoparticles mobility in combination with the high tendency of the nanoparticles to coalescence and to form immobile large sized particles at the PS domains are discussed as mechanisms of structure formation.