The movie starts with three animals(can't remember)either mice, racoons or something get captured by these guys in biohazard uniforms and taken away from there home.

I think I know what movie you are talking about! Do you remember any scenes where a noxious gas leaks into the animals homes and I believe it killed a little skunk girls parents. And the rest of the animals go on an andventure with some older animal who is like a teacher or something, to stop the humans from destroying their forest? And do they also build some kind of floating contraption? If so, I have been looking for this movie too.

If so, its called "Once upon a forest".