Set up Moz Campaigns - 1 domain, multiple langages in subfolders
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As far as I know, there is no way of preventing those subdirectories from being included in the the .com's campaign except by use of the robots.txt, which you wouldn't want to do since you do need those crawled for their individual campaigns. It would be nice to be able to "deselect" pages or folders from an existing campaign, wouldn't it. You could include that in a feature request to the Moz, if you wanted.