Hello ,
Thank you for posting in the community your question and at this time it seems like there is no other way than to manually do this one layer at a time. Please make a suggestion/wish on our road-map for sure feature. https://portal.productboard.com/7pu88c9kpmqtzt8hwg6arujh/tabs/4-under-consideration
If you did not import the geometry using collapse by material applying a unique material to each elements could take a long time, and you should considerer using collapse by material. Hope this helps.
Kind regards,
Vincent B.