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These faint lines keep appearing when I create overlapping shapes, as can be seen at the very bottom and top of the image. It should be completely white like the sides. They change slightly when I zoom in/out. The paths are completely lined up and the only stroke is on the inside of the path. I don't know how to get rid/not see them. Is this a bug? I can fix it by making my shapes slightly smaller although it seems like there should be a better way. Running Adobe Illustrator CC 2018, GPU Preview. Any help would be appreciated!!
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Try turning off GPU Performance. Click on the rocket ship in Illustrator's top menu bar to access it.
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Unfortunately that did not work. Thanks for the suggestion though.
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I am not sure what is exactly overlapping in your screendump.
What happens if you turn off Anti-aliased Artwork in Preferences General?
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So for example, in the image below, there is a purple square and a zero-fill, 8 inside-stroke rectangle. Their paths line up in the corner, but as you can see some unwanted purple lines are appearing on the outsides of the paths.
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It's probably better if you share an example Illustrator file.
You can use the CC files sharing, Dropbox, or other sharing method.
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Is there a way to attach that file to this thread?
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No, but if you save it into your CC files folder, you can share it.
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A mask will help here, you can be as finite as you want with the bleed. Draw a square over all the squares, select all, command / ctrl + 7.
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You could try if selecting both white and blue shapes and clicking Window > Pathfinder > Divide (in the lower left corner of the panel) works.