This example deletes the fourth navigation node of the second file in the active web.
Note You must apply the navigation structure to the web in order for the changes to be applied to the web.
Private Sub DeleteNavNode()
Dim myWeb As Web
Dim myChildNodes As NavigationNodes
Set myWeb = ActiveWeb
Set myChildNodes = _
myWeb.RootFolder.WebFiles(1).NavigationNode.Children
Call myChildNodes.Delete(3)
myWeb.ApplyNavigationStructure
End Sub