The embodiments fill the need to enhance electro-migration performance, provide lower metal resistivity, and improve silicon-to-metal interfacial adhesion for copper interconnects by providing improved processes and systems that produce a silicon-to-metal interface. An exemplary method of preparing a substrate surface of a substrate to selectively deposit a layer of a metal on a silicon or polysilicon surface of the substrate to form a metal silicide in an integrated system is provided. The method includes removing organic contaminants from the substrate surface in the integrated system, and reducing the silicon or polysilicon surface in the integrated system after removing organic contaminants to convert silicon oxide on the silicon or polysilicon surface to silicon, wherein after reducing the silicon or polysilicon surface, the substrate is transferred and processed in controlled environment to prevent the formation of silicon oxide, the silicon or polysilicon surface is reduced to increase the selectivity of the metal on the silicon surface. The method further includes selectively depositing the layer of the metal on the silicon or polysilicon surface of substrate in the integrated system after reducing the silicon or polysilicon surface. An exemplary system to practice the exemplary method described above is also provided.