Normally with CodeIgniter, the URI will come with http://domain/index.php/controller/method
You may have doubt to remove the index.php to have only http://domain/controller/method ..

Here is the way:
1. mod_rewrite still need to be enable in your apache server
2. Open config.php from your application/config and replace $config[‘index_page’] = “index.php” by $config[‘index_page’] = “”

3. In file .htaccess at the root of your website (should be in website root, where the system directory is) and add following line:

    RewriteEngine on
    RewriteCond $1 !^(index\.php|resources|robots\.txt)
    RewriteCond %{REQUEST_FILENAME} !-f
    RewriteCond %{REQUEST_FILENAME} !-d
    RewriteRule ^(.*)$ index.php/$1 [L,QSA]            

(My case, above changes work fine)

4. In some case, the default setting for uri_protocol does not work properly. To solve this problem just replace $config[‘uri_protocol’] = “AUTO” by $config[‘uri_protocol’] = “REQUEST_URI” from application/config/config.php

Enjoy,

Update 26/01: If you want both using index.php with URI or no, you just need to skip option 4 (using uri_protocol as AUTO)