<VirtualHost *:80>
        ServerName subdomain1.domain.tld
        [...]
        DocumentRoot /var/www/html/subdomain1
        [...]
</VirtualHost>

<VirtualHost *:80>
        ServerName subdomain2.domain.tld
        [...]
        DocumentRoot /var/www/html/subdomain2
        [...]
</VirtualHost>

subdomain1.domain.tld/a_path_for_a_cgi/ => disallow or not to find
subdomain2.domain.tld/a_path_for_a_cgi/ => disallow or not to find
subdomain3.domain.tld/a_path_for_a_cgi/ => allow