In this paper, we describe the nano-interface engineering of Co/Ge/Si system, involving interface reactions. Controlled annealing causes the Co atoms to diffuse through an already formed quantum dot network fabricated on a silicon substrate and get incorporated as epitaxial CoSi2. Additionally, we performed in situ examination of the early stages of oxide mediated epitaxial growth of Silicide at the SiO2/Si interface on a Si surface. Cobalt, deposited at room temperature on an SiO2 layer. diffuses through the oxide layer and forms epitaxial CoSi2 at the interface, preserving the original oxide surface morphology. These results suggest the possibility of an alternative and viable method to introduce functionality into nanostructures.