Yes, even in prose. I mean, depends on my POV character--if I'm writing from the POV of the parent of one of the characters, for instance, the text might refer to Scully as Dana, and Mulder as... whatever seems likely. Alan Eppes on N3, in my head/fics, calls everyone by their first names. But a superior, like Skinner, would think of Mulder and Scully, as they do.