Systems and processes for plasma-based material modification of a work piece are provided. In an example process, a first plasma in a plasma source chamber is generated. A magnetic field is generated using a plurality of magnets. The magnetic field confines electrons of the first plasma having energy greater than 10 eV within the plasma source chamber. A second plasma is generated in a process chamber coupled to the plasma source chamber. An ion beam is generated in the process chamber by extracting ions from the first plasma through the plurality of magnets. The ion beam travels through the second plasma and is neutralized by the second plasma to generate a neutral beam. The work piece is positioned in the process chamber such that the neutral beam treats a surface of the work piece.