This research work presents an intrusive methodology for debugging of embedded designs by using artificial intelligence technique. In this methodology, a cycle-accurate lossless debugging system with unlimited trace window can be used for debugging. Visibility of the embedded hardware is enhanced by an access network which also eliminates the need for frequent re-synthesis due to change in signal set. The controlling processor can configure the required network through software. A connectivity tool is developed which permits error-free connection of the DUT with the debugging system by using IP-XACT files. A correspondence analysis between the debugging results of the implemented hardware and its simulation results can be performed to speed up the debugging process. The debugging system can be partially reconfigured to any embedded design at runtime which can not only reduce the time spent on iterative place and route process of traditional debugging solutions but also makes the FPGA resources available to the user when debugging is not required