In a FLIR/laser based targeting and imaging system, the ability to recognize, detect, locate, and/or track targets in an area of interest is significantly improved by reducing the fixed and dynamic alignment errors between the IR LOS and the laser LOS. Fixed alignment errors are reduced with an improved internal boresight module and corresponding boresight method. Dynamic alignment errors are reduced with an opto-electric subsystem that employs a single pitch bearing and a common pitch/yaw afocal for both the laser energy and the IR energy. A segmented window in the system housing includes a circular EMI grid pattern which significantly reduces the amount of off-axis EMI entering the optical pathways, and improved signal processing techniques are employed to enhance the quality of the IR image after the image has been digitized.