Seems to me that some ask that question here before, try doing a forum search for 'loopback'.
But in a nutshell, I think you would create an OU with your terminal server in it. Create and link a gpo to that OU with the user settings you want and make sure you turn on 'loopback processing' (either merge or replace mode depending on what you want for an end result).
You can also link any GPO to that OU with the machine settings you want to apply as well.
When the machine boots, it will get the machine settings. Then when the user logs in they will get their user settings, THEN the new GPO with your 'lock down' settings will run and apply those settings.
This way the new GPO won't apply to their own desktops, just to the server in that OU.
Hope that helps!


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