One of the strengths of the Mixamo Auto-Rigger is its ability to produce and FBX file than can be modified further. If the character produced by the Auto-Rigger needs a tweak for your specific project, you can simply import it into Maya or any other 3d animation software, and edit it just like you would with your own character.

The process is very simple. While in Maya, first check that the FBX plug-in is loaded using the Plug-In Manager. The name of the plug-in is fbxmaya.mll. Once it is loaded, select File -> Import, and select the character you downloaded from the Mixamo website.
At this point, the fact that the character was generated using the Auto-Rigger no longer matters. You simply have a scene file with a character in it that you can edit and change however you want. You are free to add IK controls, expressions, muscle influence objects, props, or anything else you can think of.

If the skinning is not 100% to your liking, it can easily be changed. Simply select Skin -> Edit Smooth Skin -> Paint Skin Weights Tool. You can adjust the deformation in areas you feel could be improved from the initial bind.
Now, what if you’ve purchased your character and realize you want to make a change? For example, maybe you want to make some of your character’s muscles larger or smaller. Maybe someone you’re working for thinks the character’s nose is too big or his chin is not pronounced enough. As long as these changes don’t radically alter the model’s proportions, they can be done without having to re-upload your character. Simply use your sculpt geometry brush on the mesh. Your changes will be stored in an input node called tweak1 which can be turned on and off with the envelope attribute.
What if you have another version of your characters mesh somewhere else, or a character model with the same proportions that you want to use instead of your model? In Maya, as long as you have another model with similar proportions and volume, you can substitute the geometry in a rig.
Import the new model and position it exactly where the Auto-Rigged Character is. If the joints are not in the same place, this will not work well. Select your original mesh and then select your new mesh in that order. Select Skin -> Edit Smooth Skin -> Substitute Geometry and use the default settings. Your old mesh will be replaced with your new model and retain the skinning from the auto-rigger. Remember, the closer the new model is to the old, the better the skinning will transfer.
Another situation where this would be useful is if somebody else is sculpting your mesh in another program like zBrush or Mudbox. Although these programs are often used to sculpt detail that can be represented by normal maps, the sculpting will eventually begin to alter the base mesh. You can choose to extract only the normal maps from a sculpting program and put them onto your original mesh, but if you want to have a character that truly looks like what the sculptor created, you can import a new base mesh from the other application. Then, using the previously mentioned technique, replace your model with the new base mesh. This means that even after you have purchased an auto-rigged character from Mixamo, you can continue sculpting it in zBrush or Mudbox.
