Can anyone help to fix the imperfections of focus stacked.  I am trying to find a way to scan a part of a mask in a specific layer.

The mark of 15:00 in this video, this is where I'm stuck

Photography, tips and tricks: Focus Stacking - Episode 50 - YouTube

I have not looked through the video, but if you look through the files in Bridge and find the one that is stronger for the problem area.

In Photoshop, select the layers stacked focus, right click and turn into a smart object.  Add the file that you just find the stack of layers and use Auto alignment to align the new file with the smart object.  Then use a layer mask to hide out of the areas of focus on the new layer.

If you have CC, you can use Select > field on the new layer, then add a layer mask.

Tags: Photoshop

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