It sounds like these trees have been grafted as are most Japanese maples. This is a bad thing if you wish to have them as bonsai as the graft are usually bulging and will not improve over time leaving an eye sore of a reminder every time the tree is looked at, in turn ruining the illusion of a old tree.

Its hard for me to give any shaping advice without seeing the trees but I would recommend removing those grafts if you are planning on growing them as bonsai. If the trees are hardy in your zone this can be done easily by ground layering the tree. This can be done by using the tourniquet or ring bark technique and allowing it to grow a new root system of its own above the graft for a year or two in the ground outside and then removing the lower section. Harry Harington has a good article that should help explain things in more detail.

Here is a link that might be useful: Harry Air Layering