Do you refer to transparency flattening? Use a suitable PDF version. Find information on them in the documentation.
Or do you mean layers? And if so: in which context do you want to prevent flattening?
Hope they're happy with it now. Thanks!
Who is "they"? In case it's a printing bureau, don't just send them something, but ask them for the exact specifications for the job. You could even ask for a joboptions file. This would contain all the necessary options configured for their workflow and equipment.