A plasma-based material modification system for material modification of a work piece may include a plasma source chamber coupled to a process chamber. A support structure, configured to support the work piece, may be disposed within the process chamber. The plasma source chamber may include a first plurality of magnets, a second plurality of magnets, and a third plurality of magnets that surround a plasma generation region within the plasma source chamber. The plasma source chamber may be configured to generate a plasma having ions within the plasma generation region. The third plurality of magnets may be configured to confine a majority of electrons of the plasma having energy greater than 10 eV within the plasma generation region while allowing ions from the plasma to pass through the third plurality of magnets into the process chamber for material modification of the work piece.