Using htaccess to remove codeigniter index.php in a subdirectory

This should be enough:

<IfModule mod_rewrite.c>
RewriteEngine On

#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
#This last condition enables access to the images and css folders, and the robots.txt file
RewriteCond $1 !^(index\.php|public|images|robots\.txt|css)
RewriteRule ^(.*)$ index.php/$1 [L]
</IfModule>

This is what I use. My CodeIgniter also runs in a subdir.

RewriteEngine on
RewriteCond $1 !^(index\.php|images|swf|uploads|js|css|robots\.txt)
RewriteRule ^(.*)$ /ci/index.php/$1 [L]

.htaccess add:

RewriteEngine on
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule .* index.php/$0 [PT,L]

Go into application/config/config.php and clear the index page config value:

// Old

$config['index_page'] = "index.php";

// New

$config['index_page'] = "";

Solved My problem hope others too... :)