How to remove reply link?
You can implement template_preprocess_comment() in your module file or theme's template.php file. And check if comment has Parent Comment ID (pid), if yes then remove reply link.

/**
 * Implements template_preprocess_comment().
 */
function [MODULE/THEME_NAME]_preprocess_comment(&amp;$variables) {
  $comment = $variables['elements']['#comment'];
  if (!empty($comment-&gt;pid)) {
    unset($variables['content']['links']['comment']['#links']['comment-reply']);
  }
}