If I understand you corectly you want to copy the alpha channel from one image to the other image. I have just published Magick.NET 7.0.2.600 that has a new overload in CopyPixels that allows you to copy only the alpha channel. I think this will get you the result that you want:
publicvoid ConvertPictures() { var cropImagePath = @"d:\temp\BlackWithSquare.png"; var userSamplePicturePath = @"d:\temp\userSample.png"; using (var userSamplePicture = new MagickImage(userSamplePicturePath)) { using (var blackImage = new MagickImage(cropImagePath)) { blackImage.Resize(userSamplePicture.Width, userSamplePicture.Height); userSamplePicture.CopyPixels(blackImage, Channels.Alpha); userSamplePicture.Write(@"d:\temp\test.png"); } } }