The present invention describes a method and system for an interface for integrating reconfigurable processors into a general purpose computing system. In particular, the system resides in a computer system containing standard instruction processors, as well as reconfigurable processors. The interface includes a command processor, a command list memory, various registers, a direct memory access engine, a translation look-aside buffer, a dedicated section of common memory, and a dedicated memory. The interface is controlled via commands from a command list that is created during compilation of a user application, or various direct commands.