What are you trying to do with just the alpha area?
If your trying to get rid of it, I think I had a similar problem when I was playing with sapling. I kept seeing traces of the alpha in the leaf texture. I found that the alpha channel on some of the leaf textures were a little dirty. I went into gimp and there is a setting under transparency that lets you set it to all or nothing. Set it to all and you shouldn’t have those boxes around your leaves anymore.