A method for forming semi-insulating portions in a semiconductor substrate provides depositing a hardmask film over a semiconductor substructure to a thickness sufficient to prevent charged particles from passing through the hardmask. The hardmask is patterned creating openings through which charged particles pass and enter the substrate during an implantation process. The semi-insulating portions may extend deep into the semiconductor substrate and electrically insulate devices formed on opposed sides of the semi-insulating portions. The charged particles may advantageously be protons and further substrate portions covered by the patterned hardmask film are substantially free of the charged particles.