Removing index.php won't do the trick. It's .htaccess issue. See the code below.

To assure your sivlerstripe directory is set to AllowOverride All, make sure your vhost says so.

        <Directory "/var/www/html/ss">
                AllowOverride All
        </Directory>

### SILVERSTRIPE START ###
<Files *.ss>
   Order deny,allow
   Deny from all
   Allow from 127.0.0.1
</Files>

<Files web.config>
   Order deny,allow
   Deny from all
</Files>

<IfModule mod_rewrite.c>
   RewriteEngine On
RewriteBase /
   RewriteCond %{REQUEST_URI} ^(.*)$
   RewriteCond %{REQUEST_FILENAME} !-f
   RewriteRule .* sapphire/main.php?url=%1&%{QUERY_STRING} [L]
</IfModule>
### SILVERSTRIPE END ###