I protect my new trees with 1/4" hardware cloth. I bury the bottom in the soil so they don"t go under it. If you live in a high snowfall area you would want the cloth to go above the snow line. Here in Missouri we don't usually get deep snows so mine is only a foot high. Voles usually prefer a meadow like unmowed or disked place to have their underground homes. If this is what you have near your trees you will need to protect them. If you choose to use poisoned bait for them. I've found it most effective to find their hole and put the bait near the entrance. They usually clean all of the grasses or plants in a line straight out of the main entrance so you have a good line to see to help find their holes. Most of my experience dealing with them was in the central valley of California as a landscaper. No snow to deal with there so I don't know how winter long snow cover will change your experience. I found that as the trees matured and put on bark they became protected from voles. Good Luck.

Konrad and harvestmann -- thanks again for the insight. Interesting -- hadn't thought about tying up the side branch and turning it into the leader -- will give that a shot. As to rootstock -- I'm not sure about the specific rootstock, but pretty sure it is Semi-Dwarf (possibly standard)... one of the local fruit old-timers who owns the nursery where it was purchased doesn't believe in dwarfs (non-natural) here in the harsh conditions of CO. No grass or weeds... the front yard was actually scraped of grass 3 years ago, and low water local flowering plants were put in, with compost turned in and mulch elsewhere -- still a work in progress. However, it is pretty dry here... and there are some crocus bulbs around the tree (beyond the current drip-line) and 4 gooseberry and current bushes. This spring I'll setup dripline irrigation... peaches and pears in the back already have it. However, I haven't done much in the way of fertilization, and will probably auger some 2" holes and pack with compost and fertilizer this spring -- if that doesn't sound like a bad idea. Just a note -- the only reason the tree was topped was due to the fireblight... there were some small branches at that point, but being a newbie, I didn't make the connection about re-directing that other branch upward, as Konrad pointed out. Thanks for your guidance and for the link -- there's a lot to learn!

Thank you for all the wonderful answers, I hadn't even considered grafting as an option! I don't have extensive experience but I am certainly willing to try, no harm done if it fails at this point. I have a crabapple on the property as well that escaped more severe damage (but still had a nibble or two taken out of it!) so I will try spring grafting there and wait for new shoots to emerge from the existing rootstock. I've already made a trip to the home improvement store and am prepared to ramp up my defenses around the trees! I'm also planning a vegetable garden this spring so I guess it's good to know rabbits can get through the existing fence and do damage there as well. As a side note, I just realized my username is particularly appropriate in this scenario as I declare war on the wild bunny population ;) Although I'm sure my pet rabbits will appreciate the apple wood feast they're about to get, so maybe they're in cahoots....

Looks like some chewing from when the leaves were small and just beginning to grow. Not much you can do now other than keep your eyes open for new damage. I find my apple tree to be an excellent wildlife plant, it seems like just about every insect or animal enjoys eating the foliage, flowers, bark or fruit and I'm kind of surprised the tree survives.