Comment 4 for bug 171476

Hello again, I was able to create a merged png from the individual layers' png's that I extracted from my PDF, using Imagemagick:
    $ convert -page +0+0 1.png \
    -page +0+0 2.png \
    -page +0+0 3.png \
    -layers merge +repage layers_merge.png

Reference documentation: http://www.imagemagick.org/Usage/layers/#merge
I'm not sure how things would happen with other formats, but with rasters, this seems quite doable.