Kind of late reply but if anyone stumbles across this thread in the future here it is.
What I have done is use Meshmixer. It usually can't do much without messing it up completely and is kind of cumbersome to work with. But it has been very good at cutting objects in half.
Cut it up in a 3D Package? Use the Pause at height plugin to stop the printing at a certain height?
But, I would just turn it around and let the flat part sit on the plate and be super smooth.
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