This paper demonstrates the importance of incorporating and solving the machining optimisation problem jointly with part selection and machine loading problems in order to avoid unbalanced workload in the FMS. Unbalanced workload renders to ineffective FMS such that some machines on the manufacturing shop floor become more occupied than others. Since CNC machine tools employed in the FMS are rather expensive, it is mostly important to balance the workload so that all machines can be effectively utilised. Therefore, in this study, two mathematical models are presented and solved in efforts to balance the workload and improve the performance of the FMS. A two-stage sequential approach is adopted whereby the first stage deals with the maximum throughput objective while the second stage deals with the minimum production cost objective. The results show that when part selection, machine loading and machining optimisation problems are jointly solved, more practical decisions can be made and a wide range of balanced workload in the FMS can be realised with minimum production cost objective. The results also show that the available machine time and tooling budget have enormous effects on throughput and production cost.