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Go to Appearance > Menu in the ACP.

From there, you can select various items to include in your site's main navigation menu.

In the left column, you will see Pages, Links and Categories.

Since I'm using "Custom Post Types", I also see each Custom Post Type listed in between Pages and Links, which gives me the option of adding an individual post from each CPT into the website's Navigation Menu.

I'll never need to add an individual post from my CPT's into the navigation menu, so I'd like to remove my Custom Post Type boxes from the Appearance > Menu screen.

Google is taking me in circles because my question is about configuring the menu that configures the menu.

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I found the answer after I typed out the question so I'll post it at the same time.

The solution is to set the show_in_nav_menus option to false when registering the Custom Post Type.

http://codex.wordpress.org/Function_Reference/register_post_type

show_in_nav_menus (boolean) (optional) Whether post_type is available for selection in navigation menus.
Default: value of public argument

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