The layers have a z-index heirarchy, so the lowest elements (e.g. the
skeleton) do not appear above higher elements (e.g. the skin).

If I have understood your question, you mean could I create a linear
heirarchy where for example everything above a certain point could be
switched off? But there are situations where for example somebody
might want to show all the muscles of the face (elements very high up
the heirarchy) but not show the muscles of the neck (lower elements).

However, if you mean "can every layer be given a static z-index" the
answer is yes absolutely. They are already arranged into a linear
heirarchy in photoshop (all ~150 layers). However, there are subtle
rules which govern their display - for example:

"IF layer X is shown, layer Y must also be shown"
"IF layer X is shown, layer Y must be hidden"
"IF layer X is shown, layer Z must be shown and Y must be hidden" etc.

In V2 controlling the z-index and the rules was much easier, as
show(); and hide(); could be used and you could insert layers at a
specific z-index (a bit like the MCVarray, only the array is dynamic
so if a layer is removed the whole array moves down 1, messing up the
z-index order).

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