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I have created a map that has multiple layers. However, I need to print only a smaller section of the map (a zoomed in area). How do I create a PDF of only the zoomed in area? I would think I should use a clipping mask - but I can't seem to get that work over the multiple layers that make up the map.
You could try to create a rectangle the size of your zoomed area , select it and go Object > Arboards > Convert To Artboards.
File > Export > Export for Screens > Export only your just created artboard to PDF (with the preset you have selected).
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One way would be to make a copy of your file, select all layers and merge them. Create a new layer showing only the zoomed in section of the map you want to print, save as a layered pdf. In Acrobat, set the zoomed in layer properties to "print and never view" and set the other layer properties to "view and never print"*. This would only work when the pdf was viewed in Acrobat or Reader or a pdf viewer that respects layer properties.
*or simply make a 2 page pdf.
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You could try to create a rectangle the size of your zoomed area , select it and go Object > Arboards > Convert To Artboards.
File > Export > Export for Screens > Export only your just created artboard to PDF (with the preset you have selected).