how to prevent webpage instead index.php

i have installed my website build in code igniter (PHP), every url will be accessed with url/index.php/uri

i need to implement 2 rules in my htaccess :

1. i need my url looks more beautiful without index.php => url/uri
2. i need to block other uri instead index.php

i have 2 htaccess for that 2 cases

for case 1 :

# Disable rewrite for valid directory/files    
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_FILENAME} !-f

# Rewrite to index.php/URL
RewriteRule ^(.*)$ index.php/$1 [PT,L]

for case 2 :

Order deny,allow
Deny from all
<Files index.php>
    Order Allow,Deny
    Allow from all
</Files>

but if i put both together, everything i try to open will be

Forbidden
You don't have permission to access /crm/ on this server.