This feature is available for Pro papers with a custom domain URL.
Hide standard header (menu icons) and/or footer
From your Paper Settings Dashboard > Web Newspaper > Layout & appearance, then Custom Domain Options.
Click on custom header to activate it. This will hide the Paper.li Main Menu (upper left) from your readers.
Click custom footer to activate it. This will hide the standard Paper.li footer.
If you have turned your custom header to ON, you have hidden the Paper.li Main Menu icon (upper left) from your readers. So how do you, the publisher, sign in to view your Paper Settings Dashboard and Edit mode button? Click "ESC" on your keyboard to sign-in and the menus will once again be visible.
If you are editing your paper via a mobile device, add /signin to the end of your paper URL and bookmark the URL for easier access. Adding the suffix /signin will activate the log-in in place of pressing "ESC" on your keyboard.