Which item's name? Bcz, some items cann't customize with this hook.

In the better case I want to remove all the elements, so I can reorder and add some css classes on them, without breaking the menu mecanism. 

for example, the dashboard or site_notifications, can be remove, but that doesn't work with friends, messages or profile.

Messages:

elgg_unregister_plugin_hook_handler('register', 'menu:topbar', 'messages_register_topbar');

Friends:

elgg_unregister_menu_item('topbar', 'friends'); //Works fine

Profile:

elgg_unregister_event_handler('pagesetup', 'system', 'profile_pagesetup');

Also, check your activated theme. Perhaps, there are the rewrited hooks/views

Ok thanks, that works for profile and messages but not for Friends. 

That not really simple to make a theme in Elgg. It's a pity that's not standardized for all the menu items.

but not for Friends

Then override _elgg_friends_page_setup:

elgg_unregister_event_handler('pagesetup', 'system', '_elgg_friends_page_setup');

elgg_register_event_handler('pagesetup', 'system', 'my_friends_page_setup');

function my_friends_page_setup() {
    $owner = elgg_get_page_owner_entity();
    $viewer = elgg_get_logged_in_user_entity();

    if ($owner) {
        $params = array(
            'name' => 'friends',
            'text' => elgg_echo('friends'),
            'href' => 'friends/' . $owner->username,
            'contexts' => array('friends')
        );
        elgg_register_menu_item('page', $params);

        $params = array(
            'name' => 'friends:of',
            'text' => elgg_echo('friends:of'),
            'href' => 'friendsof/' . $owner->username,
            'contexts' => array('friends')
        );
        elgg_register_menu_item('page', $params);
    }
}

Yeah thanks that works fine.

I've just found this method too:

 $item = elgg_get_menu_item('topbar', 'messages');
        if ($item) {
            $item->setText(elgg_echo('dashboard'));
            $item->setPriority(200);
            $item->setSection('default');
        }

So I can manipulate the menu item without breaking the standard mecanism.

But seem to doesn't work with all, 

There is a menu hook intended just for this:

// register with higher priority so it's called after all other hooks
elgg_register_plugin_hook_handler('register', 'menu:topbar', 'modify_topbar_menu', 1000);

function modify_topbar_menu($hook, $type, $return, $params) {
   
   $remove = ['friends'];

   foreach ($return as $key => $item) {
      /* @var $item \ElggMenuItem */

      if (in_array($item->getName(), $remove) {
          unset($return[$key]);
          continue;
      } 

      switch ($item->getName()) {
          case 'profile' :
          $item->setText('Profile');
          $item->setPriority(200);
          break;
      }

      $return[$key] = $item;
   }

   return $return;

}