help to print side holes round, but not elliptic
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I haven't got a definite solution that will work at the slicer level as it looks like you already have a small layer height, but one way that works for me is to drill the holes out after they have been printed.
Another solution may be to add a little cut in the top and bottom of the circle where it goes flat. Your holes wouldn't be perfect circles but they should let you fit a bolt through.
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This guy has an excellent tutorial for modeling holes!
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thank you for ideas! i have got my own solution - it is here