Photomask repair and fabrication with use of direct-write nanolithography, including use of scanning probe microscopic tips (e.g., atomic force microscope tips, etc.) for deposition of ink materials including sol-gel inks. Additive methods can be combined with subtractive methods. Holes can be filled with nanostructures. Heights of the nanostructures filling the holes can be controlled without losing control of the lateral dimensions of the nanostructures. Phase shifters on phase shifting masks (PSMs) are additively repaired with selectively deposited sol-gel material that is converted to solid oxide, which has optical transparency and index of refraction adapted for the phase shifters repaired.