A method of manufacturing a three-dimensional object comprises: selecting a first ejector in a plurality of ejectors of a three-dimensional object printer with reference to a hardness identifier, the first ejector configured to eject a first material; selecting a second ejector in the plurality of ejectors with reference to a color identifier, the second ejector configured to eject a second material having a hardness that is different than a hardness of the first material; operating the first ejector to eject the first material toward a platen to form an inner portion of the object with the first material; and operating the second ejector to eject the second material toward the platen to form an outer layer of the object with the second material, the outer layer of the object surrounding at least a portion of the inner portion of the object.