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Problem with transparency

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When you paste, the transparent pixels are carried over to the layer you paste on to. That means that green pixels are being replaced with the transparent (erased) pixels from the blue stick-man. In the example you give, I have to assume that you have a layer beneath the stickman that is filled with all white (when I follow your steps I get the same result except that I get the 'checkerboard' surrounding the eye instead of white).

A solution might be to use "Paste into new layer" from the Edit menu.

If you want the tools to not blend with the alpha value you've chosen, you can turn off the Alpha-Blending option. There's a button on the toolbar you can do this with, or you can select the 2nd item in the Tools menu.

The Paint.NET Blog: https://blog.getpaint.net/

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