In recent years assembly systems have been under pressure to provide solutions that will enable then to deal with extremely dynamic and unpredictable market variations. Moreover, decreasing product lifecycles pose a real challenge to traditional production. To address this, new developments are required that provide highly adaptable and quickly deployable systems, and can be reusable across different products in order to distribute its cost. This motivated the introduction of Evolvable Assembly Systems concept. The introduction of this approach provides new challenges but also opportunities for current modular assembly system configuration methods. This paper reports on a new skilled based configuration methodology for evolvable mechatronic systems, which uses a process focused semantic model, as basis for assembly system configuration. The paper covers physical configuration and process configuration aspects, while highlighting the operation of the overall mechatronic system. The paper provide also a preliminary demonstration of developed tools that implement the described methodology, which highlights the potential of this approach in significantly reducing the system configuration and control deployment effort for agent-based mechatronic systems.