The authors have developed processes for producing nanoscale programed substrate defects that have applications in areas such as thin film growth, extreme ultraviolet lithography, and defect inspection. Particle, line, pit, and scratch defects on the substrates between 40 and 140 nm wide, 50-90 nm high have been successfully produced using e-beam lithography and plasma etching in both silicon and hydrogensilsesquioxane films. These programed defect substrates have several advantages over those produced previously using gold nanoparticles or polystyrene latex spheres-most notably, the ability to precisely locate features and produce recessed as well as bump-type features in ultrasmooth films. These programed defects were used to develop techniques for planarization of film defects and results are discussed. (C) 2008 American Vacuum Society.