With the advent of flip-chips, internal debug tools need to image the active regions of devices through their silicon substrates. Infrared (IR) optics can 'see' through silicon, but accurate navigation to a particular node is challenged because IR resolution is often lower than the feature size to be probed. To meet this accuracy requirement, we have developed an automated sub-resolution alignment of a device's computer-aided design (CAD) to its through silicon IR image. Automated image alignment is not straightforward because CAD and IR images differ significantly in magnification, rotation, intensity, and resolution, causing standard alignment algorithms to fail. The light diffraction of the optical system blurs and distorts the shape and size of features, causing both edge-based and intensity-based cross-correlation techniques to fail. The alignment methodology we present, consists of pre-processing (equalization) of the two images, followed by sub-resolution offset computation along with x-y confidence factors. We apply a modeled point spread function (PSF) of the optical system to the CAD image to increase its resemblance to the optical image. The application of the PSF is important in resolution-equalization, and becomes critical if 'ghosting' is present in the optical image. Using our alignment algorithm which combines image equalization, over-sampling, and cross-correlation, we demonstrate the ability to achieve 0.1 micron placement accuracy with a 1 micron resolution optical system.