How to hide folders from the site hierarchy in SharePoint Services
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I'm going to assume that you mean the quick launch bar. If not, then just leave me a comment so I can update the answer.
In a nutshell, you want to customize navigation from the site settings page. You are quick to go in and talk to NOT display any subsites. Check out this page for detailed instructions .
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One way is to use the SPWeb.Navigation class to remove all unwanted items from the Quick Launch. Check out these classes for more information:
http://msdn.microsoft.com/en-us/library/microsoft.sharepoint.navigation.spnavigation.aspx
http://msdn.microsoft.com/en-us/library/microsoft.sharepoint.navigation.spnavigation_members.aspx
Good luck.
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