When nanometer-scale holes (diameters of 50 to a few hundred nm) are imaged in a scanning electron microscope (SEM) at pressures in the 10(-5) to 10(-6) Torr range, hydrocarbon deposits build up and result in the closing of holes within minutes of imaging. Additionally, electron or ion beam assisted deposition of material from a gas source allows the closing of holes with films of platinum or tetraethylorthosilicate oxide. In an instrument equipped both with a focused ion beam, and a SEM, holes can be formed and then covered with a thin film to form nanopores with controlled openings, ranging down to only a few nanometers, well below resolution limits of primary beams. (C) 2003 American Vacuum Society.