I recently bought a Viridis Japanese Maple and I wanted to prune the bottom of the 3 foot tree, I noticed the main good size branch at the bottom, which weeps downward is the scion that was grafted on. The larger straight up portion looks very nice but I assume looking at a small akane seedling that I bought and the root stem was cut off, that the larger section is root stock from a Viridis maple , can I cut off the scion graft?, it is right on the ground. I am going to add a couple of photos to this previous post, to show the low scion ( I believe) can this low portion be trimmed off close to the trunk?

It is very common to graft weeping maple varieties onto a standard to get them up off of the ground and produce a faster tree (it's not really required, as staking the young tree can get the same results, but takes longer). The scion is the desired variety that was grafted on top, and the rootstock is, of course, the part with the roots.

If your rootstock is sending out branches, you will almost certainly want to prune them off, as the rootstock is often more aggressive than the grafted variety. The sooner you do this the better, especially in Japanese maples which don't take kindly to heavy pruning. If you do cut off anything large, be careful that you don't cut into the collar near the trunk, and that you keep the cut clean and dry.

The picture you added does help me better understand what you're asking. It looks like the branch in question is indeed part of the top graft, and not the rootstock. I believe there is a graft visible below it, but it's hard to tell for sure from here.

In this case it is just a question of standard pruning, and the information I posted above about doing so applies. There is a recently cut branch above this one at the top of the first picture which appears to have been done correctly, so copy that one if you want to cut this one off as well. Japanese maples don't like being pruned this way, but they tolerate it better the younger they are and the smaller the branch.

I agree with Paul, that's above your graft and could be cut off if you choose. If it were me I think I'd turn that tree into a "triple decker" though...

...When you plant it out face the lower (in-question) branch toward the public eye and it will become a lower level umbrella; your main foliage, which is really looking great, will be the second level, and it looks like you have an upper branch that is rising quite a bit above the middle section of the maple...this can be stem pruned along its length but leave the upper most foliage to become the upper umbrella. I know, I know, I'm weird, eh? :>)_

Shoe (jealous you have such a fine looking tree!)