Advances in FPGA-based reconfigurable computers have made them a viable computing platform for a vast variety of computation demanding areas such as bioinformatics, speech recognition, and high-end digital signal processing. The lack of common, intuitive operating system support, however, hinders their wide deployment. This paper presents BORPH, an operating system framework for FPGA-based reconfigurable computers with a goal to ease and accelerate development of high-level applications to run on these computers. It provides kernel support for FPGA resources by extending a standard Linux operating system. Users therefore compile and execute hardware processes on FPGA resources the same way they run software processes on conventional processor-based systems. The operating system offers run-time general file system support to hardware processes as if they were software. Furthermore, a virtual file system is built to allow access to memories and registers defined in the FPGA, which provides communication links with running hardware processes. Increased productivities have been observed for high-level application developers, who have few previous experiences in hardware design, to implement complex mixed software/ hardware designs on a FPGA-based reconfigurable computer running BORPH.