This paper deals with a new problem: the conjoint solution of machine assignment, job scheduling and vehicle scheduling in an FMS environment. This problem arises when we wish to reconsider the design of an FMS by evaluating its functioning with a higher model granularity. The experimental results obtained show that, in many cases, a simple reorganization of the machines can improve the overall productivity of an FMS. The evaluation model considered permits to synchronize the handling material system with the production tools, in order to minimize the time required for the production of a given set of jobs (makespan). We propose a solution approach based on an hybridized Ant Colony System (ACS). ACS integrates the knowledge of the current design of the FMS for constructing new machine assignments. Their makespan is evaluated by a black box optimization subroutine.