In a store powered by ProductCart Configurator, product categories are used not only to organize products within the store catalog so that customers may easily browse to them (e.g. Accessories > Printers > Laser Printers > Color), but also to organize all the items available for selection on the configuration pages.
Now, it happens rather often that a category that makes sense on the configuration page may not make sense in the storefront. That is: you need that category to organize selectable items on the configuration pages, but you don't need it to show when customers browse your catalog.
What's the best way to solve the issue? Select the Hide this category in the storefront feature when you add or edit any product category.
To keep all the hidden categories together in the Control Panel, what some Configurator store managers do is to create a top-level category called something like “Configurator Only Categories” and then place all of the other, hidden categories in it.