This paper develops a formal design methodology for the deadlock prevention problems in flexible manufacturing systems (FMS). We target the system that can be modelled by a particular subclass Petri net where the deadlocks in the Peri nets models resulting from insufficiently marked siphons. Deadlock prevention in a system is achieved by adding control places to make elementary siphons max-controlled. Conditions are developed under which a dependent siphon satisfies max-controlled when its elementary siphons are max-controlled. In this way the subclass is enforced to be live. Comparing with the existing methods, this policy requires a much smaller number of control places, especially for large-scale Petri nets. Finally, an application of this technique to a realistic FMS is proposed.