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.
@Fishlike
I guess you missunderstood my question.
Read what krixxuss said, it discribes the problem.
I try to change the color of the quader behind the tree in postproductions without rerendering the hole scene, this is why I need the pseudo-alphachannel of the leafmaterial.
@krixxuss
I guess you did that with “Blender intern” Renderer and not with Cycles right ?
In Cycles you can’t use the Alphachannel of a textureimage yet.
In my example the Transparency is defined by a Black and White Image. Tranparency is just pure White (RGB 255,255,255).