Various methods and apparatus are provided for merging and demerging pairs of disks. In one embodiment, pairs of merged disks are first separated and then transferred to separate cassettes such that all of the disks in the separate cassettes are oriented in the same way within the cassette. In a second embodiment, two separate cassettes of substrate disks are combined into a single cassette. The merged substrate disks may be positioned in gap merge pairs, contact merge pairs or may be equally spaced in the cassette depending upon the orientation needed for the next process.