A substrate processing method includes providing a substrate containing a first semiconductor material and a second semiconductor material, treating the first semiconductor material and the second semiconductor material with a chemical source that selectively forms a chemical layer on the second semiconductor material relative to the first semiconductor material, and exposing the substrate to a first metal-containing precursor that selectively deposits a first metal-containing layer on the first semiconductor material relative to the chemical layer on the second semiconductor material. The method can further include annealing the substrate to react the first metal-containing layer with the first semiconductor material to form a first metal silicide layer, removing the chemical layer from the second semiconductor material, depositing a second metal-containing layer on the second semiconductor material, and annealing the substrate to react the second metal-containing layer with the second semiconductor material to form a second metal silicide layer.