[eluser]Aken[/eluser]
That's the wrong place. Newer versions of CI come default with two .htaccess files, one each in the application and system folders. Their purpose is to deny requests to those folders in case someone tries to access them directly via the web browser.
If you want to remove index.php from your URLs, you add a third .htaccess in your root folder (wherever index.php is).
So, add the above .htaccess to the certifiedAnalytics folder, and replace the application directory's .htaccess file contents with: