Systems and methods are described that facilitate removing punch hole artifacts in electronic document images. When a document with punch holes is scanned, the punch holes appear as unwanted dark spots in the margin. To remove these artifacts, a blanking regions having background color pixels are placed over the punch hole artifacts and the electronic document image is stored with the blanking regions in place. A user interface is provided to permit a user to enter blanking region parameters, including x,y coordinates, diameter, reference edge from which the coordinates are measured, etc. Default settings can be stored and recalled for common punch hole patterns, which may vary between offices and the like.