RewriteEngine on
RewriteBase /your flexiauth folder/
# Prevent CI index.php
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule .* index.php/$0 [PT,L]
# Prevent user access to the CI system folder.
RewriteCond %{REQUEST_URI} ^system.*
RewriteRule ^(.*)$ /index.php?/$1 [L]
# Prevent user access to the CI application folder
RewriteCond %{REQUEST_URI} ^application.*
RewriteRule ^(.*)$ /index.php?/$1 [L]