Embodiments of silicon-based thermal energy transfer apparatus for a gain medium of a laser system are provided. In one aspect, a silicon-based thermal energy transfer apparatus includes silicon-based first and second manifolds each having internal coolant flow channels therein. When the first and second manifolds are coupled together, a first groove on the first manifold and a second groove on the second manifold form a through hole configured to receive the gain medium therein. The through hole has a polygonal cross section when viewed along a longitudinal axis of the gain medium.