<p>Ok so it looks like the only time we are actually blanking is at the end of a pattern. At the end of acquiring an image we are not currently blanking. At the end of an image, the beam is returned to (0,0), the top left corner. You can see that it is digging deep holes there. So whenever I had previously acquired an image before starting a pattern, it ends up digging a hole there.</p><p>The holes are limited in size due to sputter re-deposition ratios that change as the hole gets deeper.</p>