Very basic example of removing a node from the Content tree by a DocumentType alias.

RemoveNodeFromContentTree.cs

using System;
using umbraco.BusinessLogic;
using umbraco.cms.presentation.Trees;

public class SecrectContent : ApplicationBase
{
        public SecrectContent()
        {
            BaseContentTree.AfterNodeRender += BaseContentTree_AfterNodeRender;
        }

        void BaseContentTree_AfterNodeRender(ref XmlTree sender, ref XmlTreeNode node, EventArgs e)
        {
            if(node.NodeType == "myDocTypeAlias")
                sender.Remove(node);
        }
}

That will get me startet. Quick note: NodeType is not doctype :-) (content, media,...) but I figure it out!