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Over the years, I’ve evolved a standard structure for organizing layers in Illustrator. Whenever I fire up a new Illustrator doc, one of the first things I do is create and name the following four top-level layers:
For guides, labels for multiple mocks in a file, and other errata.
I often paste assets, screenshots, whiteboard drawings, or the like into comp. Having an explicit Scratch layer helps keep it out of the way.
It’s rare that I annotate mock-ups these days, but sometimes its necessary. Keeping them on their own layer makes it easy to hide them.
I’ll nest multiple versions (labeled “v1-foo”, “v2-bar”, etc.) in a Content folder. Usually each version represents a new approach or round of feedback.
It’s not the most sophisticated system, but it strikes a good balance between simplicity and having-a-place-for-everything, and it works for me. Do you have a layer structure? Share it in the comments!