Thanks Damaggio. As it happens, shortly after I posted I noticed the cutout option. Which worked ok, but following you pointing out that the transparency channel is in fact there in the connection editor, I have since connected to that and found a slightly better result. However, I with both those solutions as well as the two together, I find I have a new issue. My transparency/cutout map is animated. If I render in the maya renderview, it works great. If I render individual frames as a batch, it works. But when I batch render the whole sequence, the map fails and the entire object is visible. Any ideas how to get around that ?