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A multilayer run-time reconfiguration architecture (MRRA) is developed for autonomous run-time partial reconfiguration of field-programmable gate-array (FPGA) devices. MRRA operations are partitioned into logic, translation, and reconfiguration layers along with a standardized set of application programming interfaces (APIs). At each level, resource details are encapsulated and managed for efficiency and portability during operation. In particular, FPGA configurations can be manipulated at runtime using on-chip resources. A corresponding logic control flow is developed for a prototype MRRA system on a Xilinx Virtex II Pro platform. The Virtex II Pro on-chip PowerPC core and block RAM are employed to manage control operations while multiple physical interfaces establish and supplement autonomous reconfiguration capabilities. Evaluations of these prototypes on a number of benchmark and hashing algorithm case studies indicate the enhanced resource utilization and run time performance of the developed approaches.