Getting rid of index.php from your CodeIgniter URLs

Here are the steps you need to follow:
1. Create a .htaccess file to configure the rewrite engine (an example htaccess file follows at the end)

2. Set $config[?index_page?] to an empty string

3. Make sure your apache uses the mod_rewrite module

4. Make sure apache is configured to accept needed .htaccess directives

5. Restart apache and test

RewriteEngine On
RewriteBase /

#Removes access to the system folder by users.
#Additionally this will allow you to create a System.php controller,
#previously this would not have been possible.
#’system’ can be replaced if you have renamed your system folder.
RewriteCond %{REQUEST_URI} ^system.*
RewriteRule ^(.*)$ /index.php/$1 [L]

#Checks to see if the user is attempting to access a valid file,
#such as an image or css document, if this isn’t true it sends the
#request to index.php
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php/$1 [L]

# If we don’t have mod_rewrite installed, all 404’s
# can be sent to index.php, and everything works as normal.
# Submitted by: ElliotHaughin

ErrorDocument 404 /index.php

Source: http://codeigniter.com/wiki/mod_rewrite/