How can layers be organized into separate folders?

Thank you for your help. Did more searching and it cannot be done using Acrobat Acrobat Pro and AutoCAD. Bluebeam is the only program capable of creating the tree hierarchy of layers.

i am using Autocad to create the PDFs. Is there a way to control layer through CAD that would organize layer within folder when plotted to PDFthen?

It depends on your workflow. What software are you using to create the source document (e.g., InDesign, Word, etc.)?

If you want to work with the layers (OCGs) in an existing PDF, there is no user interface in Acrobat to creating the layer hierarchy that results in the tree view that Acrobat/Reader uses. You can use JavaScript in Acrobat to set the OCG order though. See the setOCGOrder document method in the Acrobat JavaScript reference for more information.