This paper proposes a novel approach to facility layout planning based on the concept of biological manufacturing systems that deal with the inherent complexity of manufacturing using ideas of self-organization, evolution and learning. A self-organization method is proposed to generate facility layout plans autonomously according to the material flow which emerges from the local interactions among production elements. A case study of facility layout planning is presented for semiconductor manufacturing, in which it is difficult to find a proper layout because of complex process flow. The effectiveness of the proposed method is discussed in terms of the accumulated traveling distance of products and the throughput.