Not quite that easy. Usually, (I think) you must actually program it. You just need to take over the controls and move the models in the way that fits with the movie. Someone correct me if I am wrong and there is a way to record character movement.
At least, that is the way with out some kind of 3rd party software. I believe in most low-poly 3-D animators (such as 3-D Canvas Pro), you can import your models, then construct your scene. You might get different effects then just taking control of your models like in FFX when a cutscene is actually just pre-controlled a game scene.
Fraggles where quite the scary lot...