How to clear already rendered "drupal messages" after successful ajax submit?
You can do it in two ways,

First One,

function hook_preprocess_page(&amp;$vars) {
  //if(CHECK FOR THE FORM PAGE)
  $vars['show_messages'] = 0;
  $_SESSION['messages'] = '';
  // END IF
}


Second One is

at the end of the form submit callback write the code like below

unset($_SESSION['messages'])


or

$_SESSION['messages'] = '';