In the past when I would export vector layers from ArcGIS each layer would be nested in a group with a clipping path over the top. As mentioned in Comments, I think this is a Question that should be the responsibility of your local Esri Technical Support to try and resolve. With @PierreP agreeing that the software behaviour change exists there should be impetus for them to resolve it. I would be keen for you to include the words written when Esri Support told you that 'it was a problem with Illustrator' into your Question, along with your reason for thinking it 'is obviously not an Illustrator problem'. This answer is an Illustrator answer since I understand that is at least partially where your problems lie. In illustrator you can set the so-called Artboard size. When you set the artboard size, everything inside the artboard 'box' will be visible in resulting files. If you want a PDF of what is in the artboard box then simply 'save as' PDF as usual. This way you can move your artboard box around and save each partial figure as a separate PDF-file for inclusion in your LaTeX document. You can also save bitmap based graphics (e.g. PNG) using the 'Save for web & devices' but when doing so you need to specify the output width/height in terms of pixels. The artboard box provides the same function in this case. 1) If necessary, sort the linework to layers based on the attributes you want the GIS data to have. The layer names will end up in a field 'Layer' in the converted data, so be as descriptive as possible. 2) Curves in Illustrator must be converted to lines before export. Use Object>,Path>, 'Add Anchor Points' command to add nodes to the curves (may need to invoke several times), and Object>,Path>, 'Simplify' command to convert to lines. 4) View in ArcGIS, and export the data to a shapefile then use the Spatial Adjustment tool (does not work with a personal/file geodatabases) 5) Use the Spatial Adjustment toolbar in an edit session to match the linework to points on a known projection (the ArcGIS Help has quite a bit about this). You can match as many points as you wish, and you can choose the method ArcMap uses to align the data. Source.