A method and apparatus for cleaning a stack of secure instruments such as banknotes is disclosed. Each secure instrument or banknote includes a substrate visual data and a security feature. The apparatus includes a chamber configured to contain a supercritical fluid at a temperature and a pressure and for a duration sufficient to disinfect or decontaminate the banknotes and not compromise the security feature and the visual data of the banknotes a structure for holding the stack of banknotes in the chamber so that the supercritical fluid circulates through and around the banknotes to remove one or more substances into the supercritical fluid and a strapping machine configured to secure a securing mechanism to the stack of banknotes.
