Model Driven Development (MDD) aims to promote the role of modeling in Software Engineering. Enterprise systems and architectures are often modeled via multiple representations. For example UML models are widely used by the designers to capture various viewpoint of the system; while formal models using languages such as CSP, Z and Petri Nets are suitable for the analysis. Model transformation techniques developed as a part of MDD can be applied to generate one model from another model automatically. This allows benefiting from the tools and techniques developed and used in multiple languages. This paper presents a method of applying MDD model transformation from UML 2.0 Sequence Diagrams to Petri Nets. The paper shows that the model transformation results in Free Choice Petri Nets. As a result, the low complexity of analysis and the synthesis techniques can be applied to the models of enterprise systems which are captured in UML Sequence Diagrams.