How Can I Secure FTP in IIS?

Microsoft FTP does not have an option for secure FTP.  You can secure the connections by disallowing anonymous logons and requiring users to log on, and/or by restricting connections by IP address or range.
If you want a more secure FTP solution, you'll need to go to a 3rd party FTP server, such as WS_FTP Pro.
http://www.ipswitchft.com/products/ws_ftp_professional/ 

To set the option to disallow anonymous logons, and/or restrict the connections by IP address or range, go to the properties of your FTP site in IIS. To disable anonymous logons, go to the Security  Accounts tab and uncheck the "Allow anonymous connections" check box.  To restrict connections to a certain IP address or range, go to the Directory Security tab, click the "Denied Access" button and then put add the IP address(es) or range(s).

Here's an article that goes through the steps:
http://support.microsoft.com/kb/816525