1. A method for performing endpointing on a sample with a charged particle beam system comprising: loading a sample into a charged particle beam system, the charged particle beam system including an ion beam and electron microscope; milling, using the ion beam, the sample to expose a first surface of the sample; forming, using the electron microscope, a first image of the first surface of the sample; milling, using the ion beam, the first surface of the sample to expose a second surface of the sample; forming, using the electron microscope, a second image of the second surface of the sample; forming a third image by overlaying the second image over the first image, the third image being a differential image formed by subtracting the second image from the first image, the third image showing the difference made from the ion beam milling to create the second surface; wherein creating the third image includes determining whether a grayscale level of one or more pixels of the first image is darker than the grayscale level of the corresponding pixel of the second image; and forming a fourth image by overlaying the first image over the second image, the fourth image being a differential image formed by subtracting the first image from the second image, the fourth image showing the difference made from the ion beam milling to create the second surface.