In this paper, an attempt has been made to address the optimum set of queues capacity, queues discipline, conveyors and transporter's speed and operational setup times in a common flexible manufacturing system (FMS) with objectives of minimisation of average stay time in queues and maximisation of throughput simultaneously. Analysis of such issues, especially when the objective functions cannot be described in mathematical terms is a complex task is focused in this paper. Here the mean of five objective functions estimated by fitness functions extracted experimentally using 36 scenarios on a valid computer simulation model. Under equal weights, the exact solution attained by the Lingo software and optimum process setting was achieved. The applicability of the new approach is ascertained through a case study involving the optimisation of real engineering system and presented using the proposed approach.