The growth of Co and Ag layers on wet-processed H-passivated Si(lll) substrates by molecular beam epitaxy (MBE) has been studied using high resolution scanning tunneling microscopy (STM) with regard to possible applications of the layers in magnetoelectronic devices. Roughness and intermixing at interfaces as functions of deposition temperature and layer thickness are key parameters for the performance of such devices. The initial growth of Co and Ag and the influence of Ag atoms on the Si(111) surface reconstructions provide insight into adatom-substrate interactions.