The Maya FBX Plug-in lets you choose to import layers from MotionBuilder without baking the animation layers. When you do this, you preserve MotionBuilder-created key framed animation layers on import into Maya. Otherwise, the animation is baked into a single animation layer.
To retain MotionBuilder animation layers as separate layers in Maya:
When you import an FBX file created in MotionBuilder, disable the Bake Animation Layers option in the Maya FBX importer. See Bake animation layers
If the option is active, the plug-in automatically bakes the animation layers during the import process.
This workflow is only for importing MotionBuilder-created FBX files to Maya 2009. Layers created in Maya do not export to FBX but are instead baked automatically.