I can only tell you what I have done and will continue to do. Chop them off at knee height, and follow recommendations for BYOC.

Here is a link that might be useful: Backyard Orchard Culture

With container grown stone fruit,I'll usually pick about four branches that have 45-60 degree crotch angles,are growing at different directions from each other,like N E S W and a little different in height along the trunk and shorten these about a third of their length.I cut the top off just above the top branch that is being saved.
Bare root,especially a whip,yes, I cut them off like mrclint does. Brady

DO NOT cut 3 yr old trees off low. You will likely kill them! If the caliper of the tree at the base exceeds 3/4" there are likely no viable buds in the first 3-4 feet. Chop it down to 2 feet and nothing sprouts out.

Bradybb has the right idea, but generally nursery container trees suffer from lollipop structure---tall, spindly and a puff of leaves at the top. Hopefully they left some branching structure for you to work with. Also hopefully it has not been staked these 3 years and flops around.

The last thing...3 yr old trees are likely to be pot bound. Hopefully you cleaned off the pot's "soil" and straitened out the roots. Otherwise the tree will simply circle the hole until it dies or gets blow over: About 3-4 years. It will look great up until then.

Brady and FN got it exactly right listen to them. If you didn't cut the roots, dig it up and spread them out. Not too late to do that, and even if it is, it might be worth doing anyway.
Sometimes they find their way out of the spiraling, but not always.

Ajax,

I've looked at your slideshow and basically your pruning height looks fine to me.

As Brady mentioned, I would tend to spread out your scaffolds a bit more. What I mean is that I try to keep 4 fingers between the pruning height of scaffolds (vertically speaking) on the trunk.

You have some scaffolds selected that will come out at the same height on the trunk. Instead of cutting some of the lower shoots you have marked, I would save some as scaffolds so the scaffolds aren't coming out at the same height on the trunk.

One thing I do differently than a lot of people is that I try to select scaffolds pretty much as flat (i.e. close to 90 degrees) as possible. I like it because it just seems easier for me to keep the tree lower and spread more. Ultimately the scaffolds start to point more upwards, but most of my scaffolds are fairly flat for the first 2-3 feet. It also makes for very strong joints. I've yet to have a 90 degree joint break, but have had narrower joints break. The only downside is that because the scaffold is so flat for the first few feet, it can make them more susc. to sunburn. It is only an issue if I prune the center of the tree very heavily in the middle of summer, otherwise I don't see any sunburn.

I wouldn't be afraid to select a 45 degree scaffold, if it was in the right place. I'm just saying given the option, I try to select flatter scaffolds.

Like Mr. Clint, I cut all my trees at knee height.

Fascist is correct in that peach trees can be killed if they don't have any live buds below the cut. However, I've found plum trees will throw adventitious shoots below the cut if the trees are healthy and strong, and the beheading is done in the dormant season.

In the case of your trees, you are leaving shoots below the cuts, so you have nothing to worry about anyway.

Lastly, I would probably leave the trees in the ground even if you didn't straighten the roots at planting. Drew is correct that it's possible the roots could girdle themselves, but I think the risk is low.

When I first started, I purchased potted trees and didn't know I was supposed to straighten out the roots. However, none of them died. Out of over 1/2 dozen trees, only one (a pear tree) grew slowly. The rest grew fine.

I still have the slow growing pear tree and it still grows slow, but part of the reason may be that I crop it pretty heavily.

I would listen to Olpea over my advice, thanks for checking in. I learn more everytime you post. I once moved a couple trees that I didn't cut the roots. One was spreading, the other was still circular, glad I dug it up! It's still with us :)
Yeah I had to move them as a dead tree had to be removed. A large 60 foot tree. The tree trimmers needed them moved, as they were afraid they would be damaged in the process. I put them back after they finished. I was going to just leave them, but had no choice but to move them. One is a really cool tree a tri-color beech. Beautiful!
The other was a yellow fruited Cornus Mas dogwood. The dogwood spread by itself, the beech was circular still. It is super hard to find. Currently i know nowhere to get one. The nursery I got it at no longer sells them. Glad i caught the problem!
Speaking of knee high. I have heard that tart cherry trees will also respond well even if thicker caliper. I only have dwarf ones that don't need cutting off.

Sorry if this takes us a bit OT, but @olpea do you ever see sunburning on flatter/horizontal branches? I never see sunburn on trunks or branches that point straight up or are angled upward, but almost all flat branches of sizable dimensions will sunburn here.

@Fascist_Nation, you seem rather certain that these plums would die if cut off at knee height. I'm interested in hearing about your negative experiences with this approach.

FN was probably thinking of peaches, I know I was. I did lose one peach from a low cut. it didn't throw anything out. I had to make a central leader on a Nectaplum, which even though part plum, only threw branches from one node. It is nice though to have them small. And the Nectaplum is fine now! I was able to cut the new central leader low and it has a fine set of low branches now. It works so well on smaller caliper limbs. I really like your 3 in one hole peaches. That is so cool! I'm going to do that at my new place. I saw some orchards that do offer you a choice of smaller trees.
The orchards and nurseries need to be educated better on BYOC. It's tough when even DWN is producing larger trees.

"olpea do you ever see sunburning on flatter/horizontal branches?"

Mr. Clint,

Actually I have seen some sunburn on the horizontal portion of branch scaffolds. However, it only occurs when I prune the tree very heavily in the summer (when the sunlight is most overhead and intense). It took me a while to learn that.

When I prune heavily in the dormant season, the trees have enough time to regrow vegetation so the scaffolds are shaded before sunlight gets intense enough to scald the bark.

I can still prune during the growing season, I just need to leave enough wood in the center of the tree to make sure the scaffolds are shaded some.

For the most part, I try to train the flat part the first 2-3 feet of the scaffold (where the sun scald can occur) then allow them to grow more upward. Of course I get more water spouts on the flat part, so I have to keep those pruned off.

Thank you very much for your comments. I am feeling alot better about what I learned and concluded with respect to my trees. I will follow your advice Olpea while I choose which of the lower scaffold limbs to keep. Thank you very much for looking at the pictures and giving me feedback, it was just what I was looking for.

So olpea, what or how do you train the limbs, what works for you best? I have seen on some pics from fruitnut some really flat limbs, pretty cool! They seem naturally to be at 45 degrees at best. Do you tie them down? I guess you need to do it early while still pliable,

I think I'm getting sunburn on flat branches in the Winter. The direct sun is really hot here, even now. The rest of the year I have ample foliage.

"Do you tie them down? I guess you need to do it early while still pliable"

That's exactly what I do Drew.

I head them all about knee height at planting. I generally receive some feathers on purchased trees, but the feathers are almost always higher than knee height. The trees look like little sticks after I plant/prune them.

I make sure there are some viable buds below the heading cut. I lost 2 peach trees a couple years ago because I thought there was a live bud below the cut, but it was dead and didn't push growth. Actually one tree completely died and the other one pushed a sucker up from the ground, which I re-grafted to the variety lost.

Then I come back in mid summer and select scaffolds. I select three scaffolds, four fingers apart vertically and as evenly spaced around the tree as possible. When I select the scaffolds at this point, I tie them down. I've done it enough it really doesn't take that long.

I carry with me old coat hangers. I straighten one out and cut it in half and bend a hook. I also carry a roll of string with me. I push the coat hanger wire in the ground and tie the shoot down. At this point if the shoot needs to be pulled forward/backward, as well as tied down, I tie it accordingly. In this way, the scaffolds are evenly placed around the tree and coming out of the tree fairly horizontal.

The ends of the shoots tend to grow upwards, but I prune so the shoot keeps growing fairly horizontal for the first 2-3 feet, then start pruning to get a little more upward growth (but still spreading outward).

By training trees in this fashion, I feel Iike I get more of a spread early on.

"I think I'm getting sunburn on flat branches in the Winter."

Clint,

I suppose it's possible. Here the sun doesn't really get intense until after the first flush of growth. I'm amazed (and envious) you have that much sunshine in winter. It must be rough :-)

Seriously though I could see pruning to be a challenge in your climate. Such a long growing season means a lot of annual wood removal (I would think). Along with more sunshine, I could see sun scald could be more of an issue.

I believe the cambium is most tender to scalding in spring as trees bud out. I see it on apples that have been butchered to the point where there isn't enough sap drawn through the wood to keep it cool at this time. I believe the ability to pull the sap is determined by the number of even tiny leaves and their exposure to the sun. If the sap moves it doesn't heat up.

Scorching that occurs in winter should be predominantly on the SW side.

I don't know if this pertains to scorch issues in the SF Valley, however. You probably also have a lot of reflected light in your small yard. It is possible that your intense pruning has something to do with the problem beyond exposing the trunk to sun. If that was the issue, white paint should solve it, which should help in any case.

Contrary to Olpea's experience, I see this injury more with dormant pruning, so maybe peaches and apples respond differently.

Olpea, when does the injury show up, immediately following summer pruning or the next season?

I seem to notice the first damage during dormant pruning (which generally occurs in the fall for me). This means the damage occurred sometime after summer pruning.

Like I mentioned, I've pretty much figured out how to control it here (i.e. leave a little more wood for shading the horizontal portions of branches in summer). In the dormant season, I still cut peach trees back to nothing.

I'll also mention, I generally see the sun burn only when scaffolds get bigger. Not sure why that is. Once you get some dead bark, it's very slow to heal. Sometimes canker sets in. Sometimes I've just lopped the scaffold off.