Patch

To patch the web server, 2 things can be patched:

1. The application part (which is the web server application, Apache web server or Microsoft IIS 6.0, depending on the type of your web server you are using)
2. The web server operating system, (either the OS is Linux or Microsoft based servers)

Get the updates or patch from the respective application provider or distribution website.

If you want to scan you web server for any vulnerabilities (should any exist), as an audit task or precaution, use Web Vulnerability Scanner such as Nikto (open source) or Acunetix Web Vulnerability Scanners (propriety, need to pay or use trial version). That’s for web server application audit, as for OS, you can audit or do vulnerability scans using Nessus.