I am not sure I understand your comment. Are you saying that your blanks naturally have high and low spots or that your blanks are smooth but after the coats of CA that the surface varies? Either way, I think some modifications to your workflow might be required.
CA should go on pretty smooth and flat. An application with a towel or some craft foam should leave possible minor texture to the surface which may need polishing out, but if it's not nearly flat after application, something is being done wrong.
Turning a blank - it isn't really finished until it is smooth and round. If you still have low spots, it's not done. However you turn your blanks - tooling is your choice, they all work including simple files or sandpaper - the blank needs to be turned round, smooth and dimensionally correct before applying finish. If you finish turning and its again not flat and smooth, something is possibly wrong with your technique. Maybe tear out is what you are seeing - ??
Am I missing something or not understanding your question?
Kevin