Does any one know how to limit Internet access into a Linux server to specific folders? I would still like users to be able to VPN in then use VNC, but not be able to access specific protected directories.

Yes, but you're going to have to provide some details, before anyone can help you.

What do you mean by "Internet access"? Lots of different protocols, and without knowing how folks are getting to your system, we can't really tell you how to set anything up. Also, if they're getting a VNC connection, it's just like they're sitting at a console....they can log in and get a desktop, so unless they're limited at their desks at the office, they're not going to be over VPN/VNC, either....

What is the need? What are you trying to accomplish? And what version/distro of Linux are you using?

If you mean http access use a .htaccess file, if you mean ssh access, use group permissions.

I have users VPN and authenticate to a Windows server. Then they VNC to the Linux server that is not setup as a domain. I am trying to prevent outside the office access to specific protected files and directories that should only be accessed from within the office on the Linux server.

Nothing you can do, based on what you're describing.

First, if they VPN into a Windows server that's on your network, they're INTERNAL at that point, when they initiate the VNC connection. And again, if they're VNC'ing over, it's just like they're sitting at a console.

You can implement a groups-based solution, like abefroman suggested, and let them connect via SSH, instead of VNC, or do a web-based solution, which could be be locked down to accept connections from only one address, and severely limit what they can access from the web page's code.