Magnetron sputtered thin film metallic glasses (TFMGs) with nanoscale heterogeneities have attracted much interest since they are amorphous materials, whose properties can be tailored. In this work, we investigated the different growth modes observed in magnetron sputtered TFMGs. We sputtered Au-based TFMGs under different working pressures of Ar, ranging from 0.4 to 10 Pa. In addition, the influence of the substrate roughness on the thin film microstructure was studied. Our results show two distinct thin film growth modes: homogeneous at low working pressures and nanostructured with mesoscopic hills and nanocolumns at higher working pressures. We also demonstrate that an increase in substrate roughness promotes the formation of nanostructures such as nanocolumns, even at relatively low working pressures. Our finding shows that the final microstructure of the film originates from a competition of surface diffusivity and shadowing effect.