Can I remove Zen Default Regions if Im not using them I want to remove regions such as 'navigation' &amp; 'highlighted' from structure/blocks just so I can visually see what is in use, and not have a list of Blocks im not using sitting there.
You cannot remove regions that have blocks in them - at least not without consequences. If you will do so, blocks will disappear and there is a chance for Drupal and PHP errors. To get rid of unneeded regions, you need to proceed in that order:


Remove all blocks from them
Remove them from .tpl files, to be sure nothing will try to render region that does not exist anymore
Now you can delete them from .info file