A method and structure is provided in which germanium or a germanium tin alloy can be used as a channel material in either planar or non-planar architectures, with a functional gate structure formed utilizing either a gate first or gate last process. After formation of the functional gate structure, and contact openings within a middle-of-the-line (MOL) dielectric material, a hydrogenated silicon layer is formed that includes hydrogenated crystalline silicon regions disposed over the germanium or a germanium tin alloy, and hydrogenated amorphous silicon regions disposed over dielectric material. The hydrogenated amorphous silicon regions can be removed selective to the hydrogenated crystalline silicon regions, and thereafter a contact structure is formed on the hydrogenated crystalline silicon regions.