In this paper, w describe partitioning large circuits into multiple chips on the programmable FPCB for rapid prototyping. FPCBs consists of areas for FPGAs for logic and interconnect components, and the routing topology among them are predetermined. In the partition problem for FPCBs, the number of wires ofr routing among chips is fixed, which is an additonal constraints to the conventional partition problem. In order to deal with such aconstraint properly we first define a new partition problem, so called the topologybased partition problem, and then propose a heuristic method. The heuristic method is based on the simulated annealing and clustering technique. The multi-level tree clustering technique is used to obtain faster and better prtition results. In the experimental results for several test circuits, the restrictions for FPCB were all satisfied and the needed execution time was about twice the modified K-way partition method for large circuits.