It sounds like your “Use URL rewriting” settings haven’t been turned on in Joomla. The good news is that our system comes ready to use Apache’s server side app called mod_rewrite. This will rewrite the ‘index.php?’ into human readable links.
To do this you need to:
1. Go to your Joomla administration panel.
2. Select Site > Global Configuration
3. Under SEO Settings set Use URL Rewriting to Yes
4. Click Save
To learn more about this please see: docs.joomla.org/Search_Engine_Friendly_URLs