A method of creating a localized deposition on a sample in a vacuum chamber having an ion source generating a positively-charged beam of ions and a separate source of primary radiation generating a beam of radiation. An ion beam from the ion source is directed toward the sample, and the primary radiation beam is applied to the sample to generate emitted electrons from the sample. The ion beam and the primary radiation beam are positioned so that the paths of at least some of the ions in the ion beam and the paths of at least some of the emitted electrons from the sample substantially overlap in space near the sample surface. The energy of the ions in the ion beam and the electric potential of the sample are adjusted to substantially prevent deposition of ions on the sample. The energy of the ions in the ion beam and the electric potential of the sample are adjusted so that a portion of the ions in the ion beam are neutralized by the emitted electrons from the sample, and such neutralized ions continue in their respective paths to deposit on the sample.