To change permission sets associated with an existing code group using Mscorcfg.mscRun the .NET Framework Configuration tool (Mscorcfg.msc).In Control Panel, open Administrative Tools.Double-click Microsoft .NET Framework Configuration. Alternatively, you can run the tool from a command prompt:In the .NET Framework versions 1.0 and 1.1, type the following at the command prompt: %Systemroot%\Microsoft.NET\Framework\versionNumber\Mscorcfg.msc.In the .NET Framework 2.0, start the Visual Studio and Windows SDK Command Prompts and type mscorcfg.msc.Expand the Runtime Security Policy node.Expand the node for the policy level that contains the code group you want to modify.Expand the Code Groups node, and then expand the tree under the All_code node.Right-click the appropriate code group and select Properties.Click the Permission Set tab.Select the permission set you want to associate with the code group from the drop-down list and click OK.

Use caspol. If you are the machine administrator, you can operate at the ‘machine’ level - which means not only that the changes you make become the default for the machine, but also that users cannot change the permissions to be more permissive. If you are a normal (non-admin) user you can still modify the permissions, but only to make them more restrictive.
For example, to allow intranet code to do what it likes you might do this: caspol -cg 1.2 FullTrust
Note that because this is more permissive than the default policy (on a standard system), you should only do this at the machine level - doing it at the user level will have no effect.