Conditional comment is a comment starts with <!--[if IE]>
which couldn't be read by any browser except IE.
from 2011 Conditional comment isn't supported starting form IE 10 as announced by Microsoft in that time https://msdn.microsoft.com/en-us/library/hh801214(v=vs.85).aspx
The only option to use the Conditional comments is to request IE to run your site as IE 9 which supports the Conditional comments.
you can write your own css and/or js files for ie only and other browsers won't load or execute it.
this code snippet shows how to make IE 10 or 11 run ie-only.css and ie-only.js which contains custom codes to solve IE compatibility issues.
<html>
<meta http-equiv="X-UA-Compatible" content="IE=EmulateIE9">
<!--[if IE]>
<meta http-equiv="Content-Type" content="text/html; charset=Unicode">
<link rel="stylesheet" type="text/css" href='/css/ie-only.css' />
<script src="/js/ie-only.js"></script>
<![endif]-->
</html>