The correct option is D Transmute
Word for the phrase 'To change shape, nature or substance of' is Option D, Transmute. Transmute is changing something completely. Option A, Modulate means to regulate or adjust. Option B, Substitute means replacement or fill-in. Option C, Remodel means to give new form or shape to something. Thus, the options A, B and C are incorrect and the correct word for the phrase is Option D, Transmute.