As a Nanometrics Systems Engineering Intern, I was asked to help the Optical Engineering team determine sources of image degradation in the spectral reflectometer optics subsystem of the Atlas II/III metrology devices. I self-taught myself core concepts in optical engineering theory and applied them to image data analysis in both ImageJ and MatLab. Using a combination of ImageJ and MatLab, I composed three software tools which allowed the company to assess the extent of image degradation in the optics head. Most importantly, I was able to assist in determining a serious system aberration in the optics due to scatter with the data I collected in my research.