Smart Manufacturing Systems inherit the work done for three decades on Flexible Manufacturing Systems (FMS) and Reconfigurable Manufacturing Systems (RMS). Their control is characterized by many residual indeterminism that
must be resolved in real time by smart functions that take into account the state of the system and the production objectives. Inadequate decisions can lead to system blockages or even dangerous situations. This study focuses
on the design of control part which is seen as a hierarchy of communicating controller layers. The study focuses in particular on the piloting layers, the implementation of the extended operating sequences and the operation
of the transport system. The different layers are modeled using Colored Petri Nets (CPN). They are structured in communicating CPN processes.