There are at least 5 problems to solve here:
- First you must remove the background on the footage of the animal
- Stabilize the position of the animal so that some prominent feature like the face does not move in the frame (this is not warp stabilizing)
- Track the movement of the camera in the shot you want to use as the new background
- Match the perspective, camera movement scale and position and lighting in the animal shot with the new shot
- Introduce motion back to the animal so the footsteps match the ground it is walking on
Removing the background on the original shot is called rotoscoping and that is the easiest part even if you have to do it by hand. After Effects has a tool called Rotobrush that may help you with this task.
The rest of the problems depend entirely on how well you have planned the shot. Your camera angles and perspective (distance from he camera) need to be matched. Stabilizing the animal so that it is locked into position in the frame makes it easier to add some animation to make the animal walk through the shot in a believable manner. Tracking or camera tracking the new footage will help, but if your camera movement or your perspective is off then the shot will look fake. Perspective is controlled buy camera position so if your documentary footage was shot with the animal 100 feet from the camera then your new background shot will only match properly if you plan for the animal to walk through the shot 100 feet from the camera. IOW, it's nearly impossible to get a good match if the animal was shot 100' from the camera buy you want the animal to walk just behind your actor that was only 10 feet from the camera.
These are the basics of compositing and success comes from careful planning. Let us know if this gets you started or if you need pointers to any further instruction.
BTW, typing Rotobrush in the Search Help field in AE will bring up some excellent tutorials on how to use that tool. The same goes for stabilize, camera track and the other steps I listed. This isn't a project that can be done easily by someone with no experience with AE. It would make a good mid term exam in an undergraduate class on visual effects after a half semester of study.
Thanks for your informative reply Rick, I will put all the time and effort in accomlishing this!
For the rotoscoping part, check this tutorial:
In the tutorial I rotoscope the river, but you can use the two shown techniques for any object. Of course, the more the objects change in shape over time, the more work it is.
Alternatively, you can film the object on greenscreen as shown here