In the scenes where the doves arrive on the ark and tar pit area, the doves had leg ties and were attached to monofilaments to keep them in place. Trainers placed the birds on their mark and placed bird seed at their feet to keep them in position. Trainers also accomplished this action in the scene where the birds land on rocks.
In the scene where Noah holds a bird in his hands and subsequently puts it to sleep with smoke from burning herbs, trainers chose a docile bird to be held by the actor. The bird was tethered to the actor’s wrist. The smoke was incense and non-toxic.
In the scene where we see a raven standing on a patch of mud, the raven was tethered to his trainer off-camera. Blue screen was used to achieve the background setting. On action, the trainer has the raven fly to a certain spot and react. He is rewarded with treats after they call cut.
All the animals we see entering the ark was accomplished through CGI.
In the scene where we see men butchering animal carcasses, the carcasses were composed of fake animals and real meat bought from the supermarket. Production provided the AHA with the proper documentation.