Due to the impending transition to 450 mm diameter wafers and efforts toward customization, an increase in setups and transient operation is anticipated for multi cluster tools in semiconductor wafer manufacturing. Clustered photolithography tools are a key class of tools facing this future. Two primary performance metrics that will be used to assess the implications of these changes are throughput and yield. This paper proposes optimization algorithms for wafer release control, which seek to improve yield by minimizing the residency time of wafers in a tool, while maintaining the maximum throughput. We also suggest heuristic algorithms to control the system in transient state. These algorithms address both transient and steady state behavior in a flow line relaxation of the system. The controls are intended to provide guidance for lower level robot controllers.