When we were working on Wolfwalkers and My father's dragon, we had to deliver pretty complex exports with several levels of separation so the Comp team could create the final scenes using Nuke. The process we used is complicated, but I will try to explain it here, so maybe some ideas could be useful for you.
This process can be simplified a lot. Many of the of the effects and treatments done in comp could be done perfectly well directly in Moho, but since this movie mixed traditional and rigged animation, we had to follow the same rules used by the rest of the teams (like Cleanup, Ink&Paint, FX, etc), in order to keep the final result totally consistent.
Ok, here comes the explanation. It will be long, sorry.
First, all the sequences we exported had "MO" (for Moho) )at the beginning and a number so the comp team could recognize the department that created them and every part of the characters.
Depending on what was the element we were exporting, we had different naming conventions for each exported sequence
MO_01_BG: Background layers. Usually animated image layers
MO_01_CO: Only the colored fills, no strokes
MO_01_LI: All the fills are white and the strokes keep their color
MO_01_LB: All the fills are black and the strokes keep their color
MO_01_MA: If it is necessary, we exported the masks as black shapes with alpha background, so comp could apply them later
MO_01_TX: Many times the animation was hand drawn, but the textures were added with Moho
MO_01_SH: For shading, all the layers are set to be white and the shading is black
MO_01_HL: For highlights, all the layers are set to be black and the highlight is white
MO_01_CS: If we animated cast shadows, they were exported as black shapes
So, let's say we are working on the scene mfd007_sc014 (My father's dragon, sequence 07, scene 14).
Once that scene is approved we have the final Moho file saved and we never touch it again:
mfd007_sc014.moho
then we save a copy of that file with "_export" in the name:
mfd007_sc014_export.moho
Inside of that "_export" file, we create all the layer comps.
Let's suppose this scene has one human, a car and a dog.
From bottom to top, we create layer comps for each one
MO_010_CO_human
MO_010_LI_human
MO_010_LB_human
MO_010_SH_human
MO_010_HL_human
MO_010_CS_human
MO_020_CO_dog
MO_020_LI_dog
MO_020_LB_dog
MO_020_SH_dog
MO_020_HL_dog
MO_020_CS_dog
MO_030_BG_Car_body
MO_030_BG_Car_wheel_L
MO_030_BG_Car_wheel_R
MO_030_CS_Car_shadow
You can see that the numbers have an extra 0 at the end. We do that just in case comp asks us to separate some part of a character.
For instance, if they need the arm separated from the rest of the body, we create the
MO_011_CO_human_arm
MO_011_LI_human_arm
MO_011_LB_human_arm
(...)
By doing that, the order of the layer comps still works, even if we added a new layer comp in-between.
Now, once we have all the layer comps ready, we save several copies of the file:
mfd007_sc014_CO.moho
mfd007_sc014_LI.moho
mfd007_sc014_LB.moho
mfd007_sc014_SH.moho
mfd007_sc014_HL.moho
mfd007_sc014_CS.moho
mfd007_sc014_BG.moho
In mfd007_sc014_CO, we remove all the layer comps that are not CO.
Then we go to the Project Settings and in Render Style we set 'Stroke style' as 'None'
In mfd007_sc014_LI, we remove all the layer comps that are not LI.
Then we go to the Project Settings, set the background color as white and in Render Style we set 'Fill Style' as 'Background'
In mfd007_sc014_LB, we remove all the layer comps that are not LB.
Then we go to the Project Settings, set the background color as black and in Render Style we set 'Fill Style' as 'Background'
In mfd007_sc014_SH, we remove all the layer comps that are not SH.
Then we select all the layers with color and open the Layer Properties. In the General tab we Colorize the layers and set it to white.

Then, if they are not already black, we select the all the Shading layers and colorize them black.
In mfd007_sc014_HL, we remove all the layer comps that are not HL.
Then the process is similar to the one above, but to set the character black and the highlights white.
In mfd007_sc014_CS, we remove all the layer comps that are not CS.
In mfd007_sc014_BG, we remove all the layer comps that are not BG.
If an animated layer has Blending Mode applied, usually we set the blending Mode to 'normal' and add the blending mode as part of the name.
For example "MO_04_BG_Car_windows_Overlay".
That way, the comp team receives the normal layer and can apply the blending mode layer later.
To finish! Some tips to make the process a bit less tedious:
- Use the Layer Window filters! They are great and can save a lot of time
- Use 'tags' in your layers names. So you can quickly filter, for example, every Highlight in the project and colorize them all at once
- You can also use layer color labels. For us, if I remember well, a Green layer means it will be colorized in white. Purple means the layer will be colorized black.
Ok, sorry for the huge message! I hope it maybe could help you or someone else some day
