Add new malicious domain to hosts file, and route to localhost:

echo 127.0.0.1 <MALICIOUS DOMAIN> >> /etc/hosts

Check if hosts file is working, by sending ping to 127.0.0.1:

ping -c 1 <MALICIOUS DOMAIN>

Ubuntu/Debian DNS cache flush:

/etc/init.d/dns-clean start

Flush nscd DNS cache four ways:

/etc/init.d/nscd restart
service nscd restart
service nscd reload
nscd -i hosts

Flush dnsmasq DNS cache:

/etc/init.d/dnsmasq restart