Production of Schenkerian graphic music analysis

hide the semibreve rests Select, press V.

I'm no expert in Schenkerian, but from reading about it, you should be able to enter notes and they will replace the rests just as in regular music. If there is a spurious rest left over then select it and press V to make it invisible. By default, invisible items are gray. You can use the View menu and uncheck Show invisible if you don't want to see them.