Methods of programming an integrated circuit (IC) such as a programmable logic device to avoid localized defects present in the IC, and ICs capable of performing these methods. As part of an automated programming process, programmable resources utilized by a user design are tested, and the implemented user design is modified to avoid any defective programmable resources that are detected. The modifications can include, for example, rerouting one or more internal signals and/or substituting a fully functional programmable resource for a defective programmable resource. These methods are carried out by testing and implementation logic included in the IC. Design information such as a software device model, test program, test data, place and route program, and/or resource swapping program can be optionally included in the configuration logic or supplied in an expanded bitstream applied to the inventive IC. In some embodiments, the modified bitstream is written to an external memory device.