I guess you want to do focus stacking. PTGui doesn't do focus stacking,
only HDR stacking. You would have to use Helicon Focus, Zerene Stacker
or similar for that.
However, if the stacks are badly aligned you can use PTGui to align them
properly. In that case you would need to create only individual layers
(not a blended panorama) and feed those to your focus stacker.
--
Erik Krause
http://www.erik-krause.de