No one really knows how Imaginary Friends are created. They are neither a result of science or magic, but some kind of strange force in between we will refer to as Imaginary Energy. All we know is that once someone dreams of a friend, he becomes real. Imaginary Energy is the only force that proves effective against Fuse and his minions. So much in fact, that Fusions based on Imaginary Friends, such as Fusion Eduardo and Fusion Coco, end up helping the heroes recover stolen items and finding Fusion lairs as a result of being partially made up of Imaginary Energy.
Fuse is aware of this weakness, therefore he and his minions are studying Imaginary Friends and the energy they are made up of by capturing Scribbles and exposing them to radiation at the Power Plant. He's also studying it thanks to the device Kevin, who was still under Fuse's control at the time, attached to Foster's Home for Imaginary Friends. Dexter was only able keep the transfer to a minimum without hurting the Imaginary Friends. The flow is eventually stopped when the hero/heroine takes on Fusion Kevin.