Show a ctools modal after form submit
You need call form to Popup by function ctools_modal_form_wrapper

Any error, message will show in popup, to check submit success you need use statement 

if (!empty($form_state['executed'])) {
    $output[] = ajax_command_replace('#modal-content', 'Thank you');
}


Or you can use ajax form to call ajax.

$form['markup'] = array(
    '#markup' =&gt; '&lt;div id="pop-up"&gt;&lt;/div&gt;'
  );
//You need markup for wrapper 
$form['submit'] = array(
    '#type' =&gt; 'submit',
    '#value' =&gt; t('Sumbit'),
    '#ajax' =&gt; array(
      'wrapper' =&gt; 'pop-up',
      'callback' =&gt; 'modal_form',
    ),
  );


And function submit form 

function modal_form($form, &amp;$form_state) {
  //Process data when form submit
  ctools_include('modal');
  ctools_modal_add_js();
  $commands = array();
  $commands[] = ctools_modal_command_display('Form Submit', 'Say Thank You');
  print ajax_render($commands);
  exit;
}