A method of enabling the use of a programmable device having impaired circuitry includes determining one or more locations of the impaired circuitry of the programmable device; generating a defect map for the programmable device based on the determined locations of the impaired circuitry; generating a plurality of configuration bitstreams to implement a circuit in the programmable device; selecting one of the plurality of configuration bitstreams that does not use the impaired circuitry indicated by the defect map; and programming the programmable device with the selected configuration bitstream.