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Most importantly, ensure that you're properly configuring both your network and software firewalls to only pass traffic that is explicitly required for business purposes. Such restrictions will resolve 99% of the port scanning activity directed at your network, blocking most attempts before they ever reach your systems. That said, a firewall alone won't completely protect you against port-scanning activity. The attacker will be able to detect ports that you've intentionally exposed to the Internet, and these can provide valuable reconnaissance information for a future attack.
The best line of defense against port scanning threats is a good intrusion prevention system (IPS). Many commercial firewalls -- both hardware and software -- come with the technology, either built-in or available as an optional feature. Alternatively, you may purchase and install a dedicated IPS to protect your network against attack. These systems monitor your network for potentially malicious traffic and block it before the traffic reaches the internal network. In a port-scanning scenario, the IPS recognizes that a particular source address is scanning your network. The intrusion prevention system then blocks that system's access and does so for a specified period of time.
More information:
Use Nmap to review your open ports.
A readers asks Mike Chapple, "What is a 'top-down' IPS sensor search?"
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