If the frames of the animation aren't already on a transparent background then you need to extract the image from the background in each frame to make it transparent.
I did not know you were using final cut for this. What you will need to do is open Imageready and Photoshop. Then copy each frame into a new document in photoshop, do any extraction you have to so that the background is transparent then goto File > Save As and save as a .tga (Targa file, used for Video). Targa's save great transparency and can be used well in applications such as final cut or adobe premiere etc.
Then use final cut pro to do the animation of the still images. You may want to create a single movie of just the animation so you can easily bring it into multiple parts of your movie where it's needed.
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