The need for agility in manufacturing systems is continuously growing. This is caused by increasing complexity and decreasing life cycles of the produced goods. This paper proposes a modular, reconfigurable manufacturing system, based on a distributed three layer architecture, consisting of mechatronic components, an IEC 61499 based distributed low level control and on top a multi agent system as high level control. Adaptivity to new demands is added by the inclusion of knowledge in the top layer. Agents are able to understand the structure of the manufacturing system and the produced goods. This enables the high level control to reconfigure the underlying system. To gain most value of this combination, agents and the low level control have to work together in an integrated environment. An interface for connecting distributed low level control and the multi agent system is presented.