[en] We report on a study of the Co intercalation process underneath the $(6\sqrt{3}\times <!--\; ??\; -->6\sqrt{3})$ R30° reconstructed 6H-SiC(0001) surface for Co film-thicknesses in a range of 0.4–12 nm using a combination of surface sensitive imaging, diffractive, and spectroscopic methods. In situ photoemission electron microscopy reveals a dependence of the intercalation temperature on the Co film-thickness. Using low energy electron diffraction and photoemission spectroscopy (XPS), we find that the SiC surface reconstruction is partially lifted and transformed. We show that the $(6\sqrt{3}\times <!--\; ??\; -->6\sqrt{3})$ R30° reconstruction does not prevent silicide formation for Co film-thicknesses  ≥0.4 nm according to XPS and x-ray absorption spectra. Our results indicate that the silicide formation is self-limited to a thin interface region and is followed by Co intercalation between graphene and silicide. Furthermore, we analyze the magnetic properties using x-ray magnetic circular dichroism at the Co L-edge. In-plane magnetization is observed for all analyzed film-thicknesses. For ultra-thin Co films, self-assembled magnetic wires with a width of the order of 100 nm form at the step-edges. (paper)