1) On your master page, create ALL of your items as controls. When you hit your target situation, have your content page access the master and hide all of the controls.
2) Create a second master page that is effectively blank. Then use the PreInit method of the page to check for your target situation and load the blank master page instead.
Protected Sub Page_PreInit(ByVal sender As Object, ByVal e As EventArgs) Handles Me.PreInit
If SpecialSituation = True Then
Me.MasterPageFile = "CustomAppBlank.master"
End If
End Sub