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Defining the capacity of the structurally controlled FMS is an extremely involved task. Most existing evaluation models fail to capture all these features that define the effective capacity of such a system. Recognizing that, under the assumption of exponential processing times, the structurally controlled FMS behaves like a continuous-time Markov chain, this paper proposes an analytical framework for evaluating and optimizing its attained performance. Due to its nonpolynomial computational cost, the approach is applicable only to small FMS configurations, but it seems to be the only known framework able to support the exact solution of the considered problem. Furthermore, it can provide the insight needed for the development of valid approximating techniques that are computationally tractable.