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Reconfigurable embedded systems are capable of changing their functionalities by dynamically adding or removing components. This enables hardware/software architectures to adapt to changes in the system environment at run-time which has been proven to be a very useful technique in multimedia applications. This paper proposes a novel methodology to combine hardware and software to a System-on-Programmable-Chip architecture to exploit the flexibility and the power of a reconfigurable system solution. A novel layered approach for the system design is presented which offers a unified interface to the application by systematically abstracting from the hardware resources. We present a prototype, where a Linux operating system is used to manage the dynamically reconfigurable hardware resources.