1. A method for detecting thickness variation of a subject material for a data storage system comprising: i.) obtaining images of a first region of the subject material and a second region of the subject material utilizing scanning electron microscopy (SEM), wherein the subject material is a material of the data storage system; ii.) image processing the SEM images to obtain a differential contrast between the first region and the second region, wherein: a.) the first region has less thickness than the second region; b.) the subject material is overlying a second material; and c.) the image processing utilizes the second material to differentially contrast the first region from the second region; and iii.) determining image intensity variation between the masked SEM images of the first region and the second region by obtaining a surface profiler image of the first region and the second region, and overlaying and calibrating the SEM images with the surface profiler images.