Q.HOW DO I GET RID OF THE RUST ON MY 2 YR CHERRY TREE?
Growing fruit trees from seeds. Trouble with cherry tree–see pics. Don’t know what happened.

Certified GKH Gardening Expert
That looks, more likely, to be multiple nutrient deficiencies. The container looks to have lost quite a bit of soil, or the tree was planted in a shallow amount of soil.
I would recommend lifting the root mass out of the container, and putting down compost and potting mix under it. This will bring the crown closer to the rim of the container. Whatever room is left, you can top off with more soil/compost mix.
This article will help you to grow cherry trees in container: https://www.gardeningknowhow.com/edible/fruits/cherry/growing-cherries-in-a-pot.htm