Depending on where you are in your retargeting workflow, you can bake the retargeted animation either to the target character’s skeleton or Control rig.
Typically, you bake animation to the target character’s Control rig when you no longer need the link to your source character or, for example, if you want to export the rig to MotionBuilder. (See Send HumanIK rigs to MotionBuilder.)
You can bake animation to the target skeleton when you finish making all adjustments to the retargeted animation and are satisfied with the results.
When baking retargeted animation, Maya uses the options you set in the Bake Simulation Options window. See Edit > Keys > Bake Simulation.
To bake retargeted animation to the target character
(Or select Bake > Bake to Skeleton > to edit Bake Simulation Options before baking.)
(Select Bake > Bake to Control Rig > to edit Bake Simulation Options before baking.)
The retargeted animation plays in the scene as Maya bakes to either the target Control rig or skeleton. For each frame of the retargeted animation, Maya sets one key on each effector or joint.