A system and method for cleaning carriers used for handling semiconductor wafers including a box cleaner having a rotor within an enclosure. Box holder assemblies on the rotor include upper and lower hooks for securing boxes to the rotor. A box door holder assembly is also provided on the rotor. The box door holder assembly preferably has a plurality of box door holding positions. Each box door holding position advantageously has a door guide and door hooks for holding a door. The box door holder assembly allows both the boxes and their doors to be cleaned with the centrifugal cleaner, avoiding the need for separate cleaning of the doors. In one configuration, the rotor is provided with an even number of box holder assemblies symmetrically spaced about the rotor and an even number of door holder assemblies symmetrically spaced about the rotor.