Add this to your htaccess file (remove the .txt extension from the file in order to use it)

Remove index.php or index.htm/html from URL requests

RewriteCond %{THE_REQUEST} ^[A-Z]{3,9}\ /(([^/]+/)*)index.(php|html?)\ HTTP/
RewriteCond %{REQUEST_URI} !^/administrator
RewriteRule ^([^/]+/)*index.(html?|php)$ http://your_site_URL/$1 [R=301,L]

Obviously change the your_site_url to the your domain in   http://your_site_URL/$1

Also remove the # before RewriteEngine On to make these changes work.