$form['some_element']['#theme'] = 'some_element_theme';

...

/**
 * Implementation of hook_theme().
 */
function my_module_theme($existing, $type, $theme, $path) {
  return array(
    'some_element_theme' => array(
      'arguments' => array('form' => NULL),
    ),
  );
}

function theme_some_element_theme($form) {
  return '<div class="my-custom-element-wrapper">' . drupal_render($form) . '</div>';
}