I usually do focus bracketing by hand of flowers and bugs. Most often, Helicon Focus does just fine. In some cases, it gets confused and I am guessing it is because of the movement of the subject. I'm not complaining but I'm wondering a few things.
Does Helicon Focus attempt to do auto aligning? Are there ways that I can help it? Are there any settings or options I can try or adjust?
Auto Align?
Re: Auto Align?
Yes, of course Helicon Focus aligns the images, without that no focus stacking is possible. Whether or not you can improve the result after shooting (i. e. without re-taking the photos) depends on what kind of a problem there is. You can go to the Helicon Focus preferences - Autoadjustments, and increase the horizontal/vertical adjustment limits. That will help if the photos are generally well aligned but the camera moved too much. If, however, something changed on the photo itself (for example, the wind moved leaves and trees) then aligning such different photos is simply not possible.