Leave them on, at least for the first growing season, more branches is better to get it to take off.
I usually then cut a few off at the bottom over a period of several years until I like the hight.

Konrad

I agree leave them for now. But I assume the graft is at ground level, permanent would be a problem mowing around and be an easy route for ground critters to climb the tree.
Sure they'll climb it anyway if they want but why make it easy for them.

When apples are young, less pruning is best.
When they settle down and produce fruit you can remove some wood when it gets overcrowded.
The last thing you want to do is start the tree producing huge new shoots, by big pruning cuts.
If the tree does get out of control with too much growth, careful summer pruning will slow them down.
Just avoid the chance of sun damage when summer pruning.

Thank you for the info. I will let the branches stay for a few years until I get new ones higher up.

I've gotten many trees from trees of antiquity, most of their trees are grown this way on purpose, it's to keep them small. They're meant to be grown as a dwarf open center bush. The idea is to weaken the central leader and get the lower laterals to grow. For me, this shape is ideal to maintain 4 or five different varieties on the same tree.

If you prefer a larger tree to give the full potential of MM-111, then cut off the branches right away, they are taking massive energy away from the Central leader. Wait for new side branches higher up, and keep a healthy central leader going.

Trees of Antiquity didn't used to prune their trees this way, older trees I've gotten from them were pruned for a pyramid shape, which is what most of my older trees from them look like now.

If you do decide to prune, be careful, the tree will take off real fast, and you will need to do more pruning next year until you get the desired shape.

I re-posted a link to a pruning slide show that explains how to properly train a young tree if you want to get it to maximum production. Also, keep in mind that early bearing has the biggest dwarfing effect on trees, so don't let them fruit unless you want a smaller tree.

Here is a link that might be useful: Penn State Pruning Workshop