Disclosed are embodiments of an ion beam sample preparation apparatus and methods. The methods operate on a sample disposed in a vacuum chamber and include steps of directing an intensity-controllable, tilt-angle controllable ion beam at a sample holder coupled to a rotation stage. The methods further include illuminating and capturing one or more images of the sample, extracting useful features from one or more images and thereafter adjusting the sample preparation steps. Further methods are disclosed for capturing sequences of images, programmatically rotating images, and displaying sequences of images with similar rotation angles. Further methods include extracting useful features from sequences of images that may change with respect to time as ion beam preparation continues.