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That is a common problem, at least with Eagle. The solution is to print to a file as black and white, then invert color with a something like Photoshop. I recall that very old versions of Eagle allowed printing a negative, but I don't have any of those versions (pre-6.0) on my machine, and you can't open anything made with a later version with those old versions.
After a little playing, you can get a .png export as the negative. Just select "export" and "monochrome" Of course then, you still need to be sure the scaling is OK with your printer.