A system and method for improving FIB milling endpointing operations. The methods involve generating real-time images of the area being milled and real-time graphical plots of pixel intensities with an increased sensitivity over native FIB system generated images and plots. The images and plots are generated with raw signal data obtained from the native FIB system. More specifically, the raw signal data is processed according to specific algorithms for generating images and corresponding intensity graphs which can be reliably used for accurate endpointing. In particular, the displayed images will display more visual information regarding changes in milled material, while the intensity graphs will plot aggregate pixel intensity data on a dynamically adjusting scale to dramatically highlight relative changes in milled material.