Problem with removing Index.php from URL

Hi Guys

I'm having a problem removing the index.php part in my website's url.

I'm currently migrating a webapplication from 1.7.2 to the new 3.0.4 Version. The Code was a bit outdated and it took quite some time to rewrite some classes and getting it functionning again. But now there is only one last Problem that needs to be solved: Removing Index.php from my URL.

To understand what is not working here a little summary of the Webapplication:
The Application shows all authorized users our companys serversystems. On the left side, one can choose to filter for OS-Versions or Operating Status or even search for specific servernames or IPs. On the right Side is a List, that updates in realtime and shows the matching Systems. If a user clicks on a serversystem in the right list, general Information about the serversystem will be dispalyed in the middle of the Site.

The problem now is, when I change the Option in application/config/config.php from $config['index_page'] = 'index.php'; to $config['index_page'] = ''; my whole site stops working. Either the search nor the filter function are working anymore. The links altough are correct, hiding the index.php page from the url like: https://www.example.ch/system/showItem/123456 which means that my mod_rewrite in the /.htaccess is working correctly (I think so). I also changed the uri_protocol option to REQUEST_URI.

I hope you guys understand my problem and also my english.
I would be glad if someone has a guess that could bring me to a solution.

Thanks in advance
Fuerro