We address the problem of determining the optimal processing times and pallet/fixture allocation in Flexible Manufacturing systems in order to minimize tool cost while meeting throughput targets of multiple part types. The problem is formulated as a nonlinear program superimposed on a closed queueing network of the FMSs under consideration. A numerical example reveals the potential of our approach for significant cost saving. We argue that our model can be Integrated Into the process planning system of an FMS to generate efficient process plans quickly.