Method and apparatus for changing execution code for a microcontroller on an FPGA interface device

This invention relates generally to programmable devices such as field programmable gate arrays, and specifically to methods for selectively replacing microcontroller firmware code. A method is disclosed for selectively overlaying portions of a default firmware code for a microcontroller of an FPGA interface device. The FPGA interface device includes a microcontroller, an on-board FPGA, and a memory having first and second pages. Upon initial power-up of the interface device, the default firmware code is loaded into the first memory page. Thereafter, the microcontroller executes instructions received from a host system using the firmware code loaded in the first memory page. Where it is desired to update or modify the firmware code, an overlay code is stored in the second memory page. The overlay code corresponds to selected portions of the default firmware code. Overlay flags are asserted for each of the selected portions of the default firmware code for which a corresponding overlay code is loaded in the second memory page. Then, during execution of subsequent instructions received from the host system, the overlay code is substituted for corresponding portions of the default firmware code for which the overlay flags are asserted.