I was able to root my fig tree through air layering method. The only problem is that this was done very late in the season, to be exact 9/24/12. My delema is do I separate the new plant from mother plant or separate it in coming spring.
Please advise. Thanks.

I had the same. I found that for me what works is not big tangled roots, but strong roots.  So, if you have them, separate it now, pot it in deep, secure to a firm wall, or post, so that the plant does not wiggle and break the new roots. mulch it, and nest the container in a bunch of mulching, so it stays warm and will continue growing 'slowly.  you will notice that the leaves in the airlayer will yellow and fall before the mother tree. protect the baby from wind draft and treat it as a tree.  water when  needed.   I  still have some out there and I am going to separate them all.  

If it is well rooted, remove it, pot it up and put it in a greenhouse or bring in indoors to finish adapting and rooting.

If the air layer was done on an in ground tree, it would definitely need to be removed now before it gets too cold. Freezing temps would kill the roots that formed on your new air layered plant.
Cut it,
pot it,
Keep it growing, like Jon said so it will get a good start.

Thanks for your advice, I will cut it and pot it indoor. You guys are the best.