This will remove unused, or categories with no inventory items assigned to them, from your on-line store. This will stop the category from appearing as a choice in the category list for vistors to your site. Below is an example of the output generated by this utility.

As you'll notice, two categories have previously been Pruned, and have been marked as so. You'll also notice that category 420, Tools, has been marked as disabled. Tools, will no longer be an option in the category tree shown to shoppers.