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When it's time to submit your job for print, the printer will tell you how they want you to supply the files. If they ask you for native files, here are some considerations. InDesign's native file format is INDD, and you need to use File > Package in order to gather up all the fonts and all the graphics that are used by the file. Just sending the printer the InDesign file isn't sufficient. So you want to give them all those necessary files just in case they need to make some modifications. Of course this can end up with a large file size because InDesign files themselves are a little large, and if you have a multiple page document and has lots of images in it; that total collection could be kind of large.
If you're working in Illustrator and Illustrator's AI format is your final file format. You have to keep in mind that Illustrator doesn't have a built-in collection feature as InDesign does. So that means it's up to you to remember to include any images that are linked to the Illustrator file or if you want to, you can also embed them in the Illustrator file. I am a fan of linking images because it's impossible to unembed images that have been embedded in an Illustrator file, and if there is a chance that an image needs to be retouched or color- corrected that's much easier if you have the linked file as a separate file.
And of course you have to remember to include any necessary fonts, in other words everything the printer needs to re-create what you did in Illustrator. If you're using QuarkXPress, Quark's native file format could be either a QXD or a QXP file depending on the version that you're using. Quark has a Collect for Output feature, and that will gather up all your fonts and all your placed graphics, and again that gives the printer all the necessary files if they need to make some modifications. If your printer asks for a PDF, the wonderful thing about PDFs is that they contain all the necessary information for print. You don't have to worry about gathering up images and gathering up fonts because everything is within the PDF, and usually that's a smaller total file size than a collection of support art and fonts as you'd have with a page layout file.
But there is a downside to PDFs, they are difficult to edit, sometimes it's impossible to fix something that's wrong with a PDF and they're unusable if they're incorrectly created. For example, if you've used low- resolution images or the file has been created the wrong size. Most printers will suggest that you submit both packaged native files and a print-ready PDF. That way if the PDF is perfect, they are ready to go. If there are problems, then they have the original file and they can make repairs, and the truth is, there is no such thing as too much to work with.
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