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In this case, please, use the new 'Subtract contour' option:

1. Select 3d inclusion (this option works in polygonal mode, not in voxel QC mode).
2. Right-click on it, in context menu select 'Subtract contour'
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3. Draw a contour you want to remove:
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4. Right click and select 'Finish'. After that you will see something like this:
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