PartyNeon is right, there is no way to control what links appear below the root domain, it's called links list and if you want to remove any of it, you can do it through the Google Webmasters Tool. And, I'm with PartyNeon, that these links appear due to high user engagement and if the site is properly structured.
Usually, if you have a navigation menu, most of the time some of these menu items will appear as link list...