Join our CAD community forums where over 25,000 users interact to solve day to day problems and share ideas. We encourage you to visit, invite you to participate and look forward to your input and opinions. Acrobat 3D, AutoCAD, Catia, Inventor, IronCAD, Creo, Pro/ENGINEER, Solid Edge, SolidWorks, and others.
The 3D format supported in Acrobat 3D is .u3d. This is what is used in the 3D annotation. The Acrobat 3D product converts many different 3D file types into a .u3d file on its way to becoming a 3D annotation inside of Acrobat. The .u3d spec does not support layers in the way I believe you want to use them. I believe it may store or convert this layer data as some kind of meta data, but I don't think that would be useful in this sense.
MicroStation uses a "pdf.plt" printer driver to produce a PDF file with a "levels" tab, which enables the user to turn on and off display of individual CAD file levels within the PDF file. Is this what you need to do with levels?