Methods and systems are provided for protecting a circuit design for an integrated circuit. Logic circuits are identified in at least a portion of the circuit design for replacement. The logic circuits in the circuit design are replaced with a bitstream and configurable circuits that comprise memory circuits. A transformed circuit design is generated for the integrated circuit that comprises the configurable circuits. The configurable circuits in the transformed circuit design perform logic functions of the logic circuits when the bitstream is stored in the memory circuits in the configurable circuits.