It means exactly what it says...you are special to him. Depending on your relationship with him it could mean that your special to him in a romantic way or it could mean your special to him as a friend.
It means what he wrote. Guys don't do that 'cute little hint' thing that girls do. He wouldn't have said that if he didn't mean it.
..that you're very special to that guy..?
it means a good thing, ha. x