At the initial stages of PE-ALD of Co, our results show that the N2/H2 plasma pre-treatment on the Si substrates would generate surface NHx terminations, which promotes Cp ligand elimination and shortens the incubation period, but the resulting surface should not have a thick Si-NHx terminating region, which can be avoided with a short plasma pulse. The reactivity is highly dependent on the Si (100) substrate terminations, which can also be utilized for area selective deposition. For Ru deposition, RuCp2 is not a useful precursor, showing highly endothermic ligand elimination reactions on all Si terminations.