A method and system for cleaning a secure instrument, such as a banknote, including a substrate, visual data and a security feature, including exposing the secure instrument to a supercritical fluid at a temperature and a pressure and for a duration sufficient to clean the substrate and not compromise the security feature and the visual data, wherein to clean the substrate includes to remove one or more substances from the substrate into the supercritical fluid. The substances removed from the substrate may include contaminants, dirt, sebum and pathogens.