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This is the proper way to bake the FBIK in maya:

1. First of all, select all of your joints in the outline.
Then select the transform and rotate channels in the attribute editor.

Pic of step one:

2. Then go to edit>keys>bake simulation option box.
Make sure that Hierarchy is “Selected”, and Channels is “From channel box”.

Pic of step two:

3. Remove your effectors and your fbik. Save your file, import it to Unity.

Above taken from the Unity Forums here:

http://forum.unity3d.com/viewtopic.php?t=11211

1) Baked the Animation. Edit>Keys>Bake Simulation (made sure to set “Below” but left other defaults alone.
2) Deleted leftover constraints nodes.
3) Deleted IK Handles and Effectors
4) Deleted Non-Deformer History of main mesh

In general, we’ve found that the baking IK with Unity’s import options works well and it’s nice to not bake in Maya so that you can then go back and make adjustments to the animation.

But watch for these things:
1) Bad (or unnecessary) history (you had a polySoftEdge and polyNormalPerVertex on the main mesh down stream of the skinCluster node)
2) Constraints. Any Point or Orient Constraints cause problems. For that matter, most anything that uses the “move this, and use it’s attributes to drive another object’s attributes” paradigm causes problems. So, Driven Keys don’t work and cause problems. The obvious exception is parenting. So if you had parented your Root to a NURBS curve, and then animated the NURBS curve, you’d be fine.
3) “Clean” animation. This was tough to track down any reporoducable (sic) problem. But generally, animating by hitting the “s” key in Maya creates some monster collections of data. You can avoid this by using “shift-w” to set Translate Keyframes, “shift-e” for rotation, etc..Alternately, in the Channels Box, if you right-click on attributes that won’t animate (scale for instance for something like the foot IK), and choose Lock and Hide Selected; you can then animate with “s” as it will only place keyframes on the available channels/attributes.

Above taken from the Unity Forums here:

http://forum.unity3d.com/viewtopic.php?t=18120