A system and method for storing items and tracking usage of items in a user configurable medication dispensing cabinet is disclosed. Items are stored in a tray or drawer having user-adjustable storage spaces. A graphical user interface comprising a touch screen enables users to rapidly customize the layout of storage spaces, which allows a wide variety of shapes and sizes of items to be stored in the tray. A kit of items that are identified in advance may be removed more efficiently by ordering removal based on the location of the storage spaces in which the items are stored. Items not identified in advance may be removed and tracked more efficiently through the use of the graphical user interface or a scanner for reading machine-readable identification tags on the items or the storage spaces. Bar codes and RFID devices are contemplated for use as identification tags.