Abstract: The present disclosure provides a multi-substrate handling system having an alignment apparatus capable of positioning each of a set of substrates in predetermined orientations for transfer. A buffer chamber is configured to receive and condition the set of substrates which are disposed on a substrate carrier. A first transfer assembly is configured to transfer the set of substrates to and from the buffer chamber and is capable of transferring each of the set of substrates from the alignment apparatus to the carrier in the buffer chamber. The carrier includes a plurality of modules capable of securing the set of substrates. The system includes a second transfer assembly having at least two robots configured to transfer the carrier of the set of substrates between the buffer chamber and a process chamber. The process chamber is capable of processing the set of substrates using different process parameters for each substrate.