#Scribus is an open source desktop publishing system, which can export pages to a multi-layered pdf. I hope #QGIS will be able to create multi-layered pdf files too in near future.
@Igormay which layer format? Qgis can already export layered pdfs if you use the geospatial pdf export option. This works in most pdf viewers, but not adobe illustrator cos it has some other undocumented pdf layer spec 🙄