An apparatus for hydrogen and helium implantation is disclosed. The apparatus includes a plasma source system to generate helium ions and hydrogen molecular ions comprising H₃⁺ ions. The apparatus further includes a substrate chamber adjacent the plasma source system and in communication with the plasma source system via one or more apertures, an extraction system to extract the hydrogen molecular ions and helium ions from the plasma source system, and an acceleration system to accelerate extracted helium and hydrogen molecular ions to a predetermined energy and direct the extracted helium ions and hydrogen molecular ions to a substrate.