Adding or removing even a small amount of soil around a tree, or changing the grade around the tree, has the potential to injure or weaken the tree and, in extreme cases, kill it.

A few inches of organic matter-rich, high-quality soil added around a healthy, vigorous specimen will often have little negative impact, but adding 4-6 or more inches of soil will typically bring more serious consequences.

If it under 4 inches of fill dirt, spread it around the entire root system. I'd keep the dirt away from the apple's trunk. Don't bury the graft union of the apple.

If you have more than a couple of inches of fill dirt, I would dig out and replant the trees higher in the soil. Two year-old plants will not suffer too much if you dig them up and replant during the wet season. If you break any roots, use pruners to make a clean cut.