Reconfigurable Systems-on-Chip (SoC) consist of large Field-Programmable Gate-Arrays (FPGAs) and standard processors. The reconfigurable logic can be used for application-specific coprocessors to speedup execution of applications. The widespread use is limited by the complexity of interfacing software applications with coprocessors. We present a virtualisation layer that lowers the interfacing complexity and improves the portability. The layer shifts the burden of moving data between processor and coprocessor from the programmer to the Operating System (OS). A reconfigurable SoC running Linux is used to prove the concept.