Alienation is going to be found in the characterization of Holden. If the definition of "alienation" is seen as being divided from one's social setting, Fundamentally, Holden finds himself alienated from the world around him. Holden is alienated from life at Pencey Prep, where his "hatred of phonies" creates a barrier from him being able to fully immerse himself in that social setting. Disdain for people like Stradlater and Ackley, as well as misunderstanding people like Antolini and Jane helps to further this alienation. Holden is alienated from his social condition because he cannot bring himself to be immersed in it. He cannot bring himself to being an active participant in this world. He is passive within it. (The narrative shows him to be passive aggressives, but to the outside world, he is merely passive in it.) There is a barrier- namely, his own maladjustment- that prevents his full involvement in this social condition.
Holden is further alienated through his own frame of reference. For Holden, all of his social interactions are predicated with a part of his being interacting and a part withholding full communication. Holden's social interactions are ones through which there is "one foot in, one foot out." In his mind, this prevents him from being hurt or being manipulated. However, the reality is that this furthers his alienation because it prevents a full sense of social communication and meaningful interaction. His dislike of what he sees in New York and his fairly intense dislike of authority figures are further evidence of his alienation being a reflection of his own state of being.
The only exception to this would be his love of Phoebe. It is here in which he is not alienated. He is fully immersed with his love of Phoebe, a realm in which he does not see hurt. From his love with Phoebe, he is able to envision a realm in which he is not hurt, and one in which he has overcome his sense of alienation. Consider the point in which he tells his sister of his dream:
I keep picturing all these little kids playing some game in this big field of rye and all. Thousands of little kids, and nobody's around—nobody big, I mean—except me. And I'm standing on the edge of some crazy cliff. What I have to do, I have to catch everybody if they start to go over the cliff—I mean if they're running and they don't look where they're going. I have to come out from somewhere and catch them. That's all I'd do all day. I'd just be the catcher in the rye and all. I know it's crazy, but that's the only thing I'd really like to be. I know it's crazy.
It is here in which Holden does not show reflect an alienated sense of being in the world. Holden is not alienated in this context. He is fully immersed in the world around him and is fully operational within it. He seeks to be an active part of this realm, and it is where he sees it as "crazy." This would be where Holden has overcome his alienation and his sense of division with the world.