When scanning overlays the scanner doesn’t know which part of the image you want to be transparent. But FlipBook has an option to create an alpha channel and make anything that is pure white, or close to it, transparent. Just put a checkmark in the Overlay checkbox and then you can set the keying value. Keying is a term for making part of the image transparent. If the value is set to 255 then only pixels that are pure white will become transparent. Usually a number that’s a little lower will produce better results. Experiment to find the number that produces the results you like best.
In addition to making the white pixels transparent, FlipBook will also put a slight blur on the edge to produce a smoother transition. This is a quick and easy way to make the white part of your images transparent but will not produce perfect results in all cases. For better results you will need to buy a program that specializes in creating alpha channels or make your own in Photoshop.