The closest thing I've seen to this a movie called The Invisible... but it's really bad imho :/
There's an Anime called Another where in a somewhat similar way to the Ibuki Fuuko arch there's a girl who becomes visible only to the main character. But I didn't like it much either because it's very much like those teen japanese ghost horror movies; which I personally don't like.
Smilar themes appear in other animes... like in the Haruhi movie, an episode of Mushishi or one of the Higurashi OVAs, but they'd require watching the series first (all of them worth watching though imho). It seems to be a very recurring theme in anime, but I don't remember ever watching a good movie with such a plot. The closes things I've seen to all of this is the when in psychological thrillers such as Shutter Island, The Wickerman, The Machinist, The Others, etc. some characters become only visible to the main character's eyes to confuse you so that you don't know if everyone is conspiring against him or he has become crazy and is imagining people.