A system is provided for programming a configurable semiconductor device. The system includes a programmable controlling device, a programmable computing device, a communication link, a configurable hardware device, a design tool with first computer program code, and second computer program code. The configurable hardware device has memory with a plurality of memory locations and coupled with the programmable controlling device via the communication link. The design tool includes first computer program code embodied in a programmable computing device. The second computer program code is generated at least in part by the first computer program code and is embodied in the programmable controlling device for: a) applying configuration data to selected memory locations within the configurable hardware device to configure the configurable hardware device; b) determining a location of a subset of at least one of (i) the programmable memory locations in the configurable hardware device and (ii) the configuration data to be modified; and c) determining a new data value to be applied to the subset of at least one of (i) the memory locations in the configurable hardware device and (ii) the configuration data. The design tool provides at least one of configuration data, address data, and a data value algorithm usable in performing at least one of a), b), and c). A method is also provided.