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 ###