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 X-ray 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.