A method and system for electronically clearing financial instruments through a clearing system in which a per item cost of clearing instruments varies with the time of day. Files of items containing data scanned from financial instruments including an amount of each instrument may be received by a control system that may apply a rule to sort the items by determining whether the item be stored or forwarded for clearing. The rule may include a step of determining whether an amount of the instrument exceeds a predetermined value or meets a certain criteria, and if so, forwarding the instrument for clearing without storage. If the amount of the instrument does not exceed the first predetermined value or meet the criteria, the system may store the item for forwarding at a later time when the per item fee for clearing is lower.