This paper develops a deadlock prevention policy for flexible manufacturing systems based on siphons of Petri nets and the theory of regions. We first develop a polynomial algorithm to get partial siphons in an S/sup 3/PR. The deadlock control approach consists of two stages. The first, called siphon control, is to add, for each siphon we get, a monitor to the original net model. At the second stage, we don't explicitly control the siphons which may include some siphons in the net model, and the control induced ones generated due to the addition of monitors but rather utilize the theory of regions to derive the liveness enforcing Petri net supervisors such that deadlocks can be prevented. Finally, an example is used to illustrate our approach and advantages over the existing methods.