Disclosed is a system for moving substrates in and out of a manufacturing process. The present invention comprises an automatic transfer device for automatically transferring a cassette that stores substrates, a manual transfer device for transferring the cassette according to instructions of an operator, and a process apparatus for performing predetermined jobs on the substrate stored in the cassette, wherein the process apparatus comprises: a port on which the cassette is temporarily placed by the automatic transfer device or the manual transfer device; a loader which has a sensor to receive a communication start signal transferred from the automatic transfer device when the cassette is transferred by the automatic transfer device; and a job table on which actual jobs on the substrates, stored in the cassette, are performed, and wherein when the cassette is placed on the port, the process apparatus checks whether the communication start signal is received by the sensor, and when the signal is received, it is determined that the cassette has been transferred by the automatic transfer device, such that the process apparatus is set in an automatic transfer mode, and when the signal is not received, it is determined that the cassette has been transferred by the manual transfer device, and therefore, the process apparatus is set in a manual transfer mode. The present invention improves productivity and efficiency.