In one embodiment, a method for improving the alignment of CAD data to optical imaging data, such as LSM and LVI images of integrated circuits is disclosed. Image reconstruction techniques are applied to optical images, such as laser voltage images (LVI), laser scanning microscope (LSM) images, or emission images, to produce reconstructed images which may have higher resolution, increased signal-to-noise, or other enhancements. Multiple CAD pattern layers are processed to generate second CAD images more closely corresponding to the appearance of the reconstructed images. Alignment of the reconstructed images to the second CAD data may be substantially more accurate and precise than alignment of the initial optical images to the CAD data—in some cases this improvement may make the difference between a successful alignment and a failed alignment.