I saw this posted about a year ago (Can QGIS preserve layers when exporting to PDF?) but figured it was worth asking again -- is this possible? My usual workflow with ArcGIS is to export to AI then edit the layers that way, is there some way to do that from QGIS? Now I just get everything in one huge layer. Thanks.
2 Answers
See if this helps with the Illustrator part of your question:
Losing large portions of elevation contours from QGIS to PDF
Short answer on QGIS layers to PDF layers support, not yet. My guess would be some form of support might show up by way of the GDAL/OGR providers.
While the version 2 GDAL driver and OGR driver have model-tree layer support for writing PDFs, it's not the same as 'regular' PDF layers.
Sample of Model-Tree (not produced with GDAL/OGR)

The GDAL driver appears to have support for layering an OGR data source over a raster layer (see OGR_DATASOURCE).
Here is some recent discussion on the subject:
GDAL - Dev - [gdal-dev] Geospatial PDF with OGR_DATASOURCE
And some discussion on regular PDF layer support:
GDAL - Dev - [gdal-dev] PDF selective layer sample wanted
There are other libraries, like Cairo and Poppler, but I don't know if anyone is integrating them with QGIS.
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The GeoPDF support is now included in GDAL 1.11 for vector and raster data, but QGIS is not yet able to use it. It can only export a single raster layer to PDF. – AndreJ Nov 07 '14 at 15:14
You could try to export it as svg using the simple svg plugin. It keeps layers intact. Then Import the svg in AI. You could then save as PDF from AI if that is your final format.
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I know this was forever ago, but I tried that and it put everything into one layer. This was using the print composer, I can't see how to export it otherwise. – wisemana Sep 17 '14 at 19:22
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