How do I remove unused links?
There is two options using a custom module:


Disable access to this path using hook_menu_alter()

function MYMODULE_menu_alter(&amp;$items) {
  unset($items['user/register']);
}


This option will send the user to an access denied page.
Redirect the user to the home page (or another one)

function MYMODULE_module_menu_alter(&amp;$items) {
  $items['user/register']['page callback'] = 'MYMODULE_go_home';
}
function MYMODULE_go_home() {
  drupal_goto('/');
}


Inspiration: Disabling /node view and other hidden views in Drupal?


PS: I'm not sure why you want to remove /user ? For this special path you can also use hook_user_view().