The inherent reconfigurability of FPGAs enables us to optimize an FPGA implementation in different time intervals by generating new optimized FPGA configurations and reconfiguring the FPGA at the interval boundaries. With conventional methods, generating a configuration at run-time requires an unacceptable amount of resources. In this paper, we describe a tool flow that can automatically map a large set of applications to a self-reconfiguring platform, without an excessive need for resources at run-time. The self-reconfiguring platform is implemented on a Xilinx Virtex-II Pro FPGA and uses the FPGA`s PowerPC as configuration manager. This configuration manager generates optimized configurations on-the-fly and writes them to the configuration memory using the ICAP. We successfully used our approach to implement an adaptive 32-tap FIR filter on a Xilinx XUP board. This resulted in a 40% reduction in FPGA resources compared to a conventional implementation and a manageable reconfiguration overhead.