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Abeman21, we've got a feature request on doing that - I'll attach your post so the rest of the team will know you're one of the folks that would like to see that added. Thanks!

MatthewS: in case it helps, your alternative is technically possible, given that OmniGraffle gives you per-layer control over printing in the sidebar. (Specifically, click the printer icon that appears just beneath each layer's name to allow/prevent printing.)

Obviously, on a canvas with many layers, that may still be a lot of clicks to accomplish what you're after. I'll look for a feature request that covers that and either attach you or file one on per-canvas control. Thanks!