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I need to make a map with selectable layers. I am using ArcGis and so far I am able to create a map that has some selectable layers and most labels are selectable. The PDF looks like below:

Only some layers are selectable, all labels are selectable

But I need to figure out how to make the layers stay separately rather than in folder so that they look like this:

All layers are selectable

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If you have access to Illustrator you can do this. Export from ArcGIS to .ai Illustrator file. Open in Illustrator. Most of your layers will probably be listed as sublayers to the main layer 'Layers'. Open 'Layers', grab all the sublayers and drag them outside of 'Layers'. Save as a .pdf and you should have what you are looking for. See below.

enter image description here

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It is not possible to do that. You will find that there are a number of limitations in the PDF files created using ArcGIS for Desktop.

If you would like to see more flexibility, then I recommend that you visit ArcGIS Ideas to either vote for or create suitable enhancement requests.

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