A clustered substrate processing system comprising one or more lithography elements, each lithography element arranged for independent exposure of substrates according to pattern data. Each lithography element comprises a plurality of lithography subsystems, a control network arranged for communication of control information between the lithography subsystems and at least one element control unit for transmitting commands to and receiving responses from the lithography subsystems. Each lithography element also comprises a cluster front-end for interface to an operator or host system. The front-end is arranged for issuing a process program to the element control unit, the process program comprising a set of predefined commands and associated parameters, each command corresponding to a predefined action or sequence of actions to be performed by one or more of the lithography subsystems, and the parameters further defining how the action or sequence of actions are to be performed.