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May 22, 2015 at 8:58 PM
Trying to do exactly this with Magick.NET

convert.exe overlay_figure.gif overlay_mask.png -alpha off -compose CopyOpacity -composite overlay_removed.png

I have tried using MagickImageCollection, adding both images, but don't see options for -alpha and -compose, the best I could find was:
                result.HasAlpha = false;    
                result.Compose = CompositeOperator.CopyAlpha;
May 22, 2015 at 9:00 PM
It would have helped had I just searched a little first:

Sorry about that