A method and apparatus for preventing substrate damage in a factory interface. In one embodiment, a method for preventing substrate damage in a factory interface includes the steps of receiving an indicia of potential substrate damage, and automatically preventing substrates from moving out of a substrate storage cassette in response to the received indicia. The indicia may be a seismic warning signal, among others. In another embodiment, a method for preventing substrate damage in a factory interface includes the steps of moving a pod door in a first direction to a position spaced-apart and adjacent a pod, and moving the pod door laterally in a second direction to close the pod. The lateral closing motion of the pod door urges substrates, which may be misaligned in the pod, into a predefined position within the pod.