I am going to be pruning a ton of trees this fall that were just started this spring. Most are over 3 feet tall and have 1 trunk. What do you do in this instance? I want to keep a tree form but I don't want to end up with one trunk 12 feet tall either. The taller ones I am air layering.
Thank you in advance for any suggestions.

Get yourself a backup tree, just in case.......

Hi Sal,
I have back up's for almost all of them. I kept at least 2 and sometimes 3 of the rooted cuttings. There was a thread this summer about exactly that. We're all scared to death of losing a variety it seems :)

If they are single trunks it will be pretty easy. In late winter before bud break just top the tree at the height 6 inches above where you want branches to develop. Cutting the top will induce branching.

How short do you cut them? I don't know if there is a generally accepted or "perfect" height to cut them to. That is part of my confusion.

It depends on what you want. If a bush shape, lower growing, easier to reach, prune down to 12-18".

If you want a tree to walk under, grow a single trunk to the height you want the branches at.

if something in between, prune accordingly.

My limited experience (mostly accidental) would suggest that you will get more branching if you prune just after breaking dormancy. White single shoots) pruned when dormant tend to break only the apical or top bud, or maybe the top 2. If the tree has broken dormancy, they seem to break more buds if pruned the, perhaps because the tree has already ramped up to full speed (sap flow).

This will be my first year to prune too.  Thanks for starting this thread Tami, it has been very helpful.

Thank you Jon. I have just gone out and had a good look at my mini orchard. I will be keeping most everything in pots long term so I will probably trim everything between 18" and 3' to get a mini tree that I can reach the top of but have room at the bottom to water and work the soil. I'm feeling much better about taking the nippers to them now with a firm game plan in place.

The pencil VdB I got from Burnt Ridge earlier this year has been air layered in half and I'm still having trouble getting it to branch. It is heavily infected with FMV so that, I'm sure, is a contributing factor.

I think I may air layer the parts I want to prune just so I can share them with my friends. Mike (newnandawg) posted a link to some giant cubes for air layer cups earlier 
http://www.kinsmangarden.com/category/s?keyword=q+plugs
I bought several of these and have made my own cups with 32oz deli containers. The lids can be cut to snap on as well and I filled the extra space with soil. They are working like a dream. I pull them open a bit and put some dip n grow on them and slap it on the limb and cover.

Tami, I dug out some photos of an air layer I did this summer,
which taught me some things.
Pic #1 shows the 6' tall whip I got in a trade in March.
There was no branching at all. I pinched, and I got some
branching, but the plant was still too tall, so I decided to do
an air layer.
Pic #2 shows the top section of the air layer after it established
itself as an independent plant.
Pic #3 represents the base, or original plant.

I think the scaffold branches in pic #2 may be a little too
close to each other, whereas the base plant, with its nodes farther
apart, will have a stronger shape.
In tree pruning, one doesn't want to have scaffold branches so close
together.

I might not have pinched the upper section of this
plant if I were to do it again, but I've learned a lesson. I'll have to
keep that plant small, or prune a couple of branches out.

Looking at the nodes below the pruning cut, and picking
a spot where they aren't clumped together may be a good
practice if you're planning on a fruit tree shape.

Everything I've read about pruning brings me to the conclusion
that I should train branches to a 45 degree crotch angle,
prune only the extra vertical leaders, and leave one leader to branch
out about 2' above the lower scaffold branches.

I'm going to be picturing 2 wagon wheels,
one at 3', with 4 or 5 spokes, the other at 5', with 3 spokes.

I'm also considering using wax on my cuts, instead of tar.
I'll be keeping in mind that wherever I cut, I'll be stimulating
the tree to sprout branches from the nodes 6-8" below that
cut, so I won't cut above a node that faces up, unless
I plan to spur prune that spot every year, like a grape vine.

Long winded observations. Sorry.

Ruuting,
Long winded is exactly what I was hoping for when I posted this thread. Long winded and pictures are what teach us how to do things.
I am quite taken with picture #2, that's exactly what I have in mind.
Thank you so much!

Tami,
I started a topic about pruning earlier this season. It has a basic diagram and procedures. It should answer some of your questions. The one thing that you did not mention was your planned tree height. That is the determining factor as to the height of your main trunk (the height of your first pruning cut). The taller (higher) the main trunk, the taller the final tree height. If the main trunk is cut very short (less than 12 inches) you will get a Bush form tree.
Good Luck.

<edit> If the cuts will be at 24 inches, the final pruned tree height will be 6 - 7 feet. You should be able to reach the figs easily because the fruiting branches will be below that height.

Pete,
I read your thread and saved the pictures it was very helpful. I guess my dilema was how long to cut the main branch. I want to maintain a tree form and have room underneath but still be able to reach the top. I have to keep the trees in containers except for a very few in ground so that the pot size has to be considered as well. As my son says "you are a tiny little person" so I have to adjust for that as well. I don't want to have to drag out a ladder!
Funny thing is....when I started getting these I thought I had a few years before worrying about this. These grow really fast! I think most of my cuts will be around 24" and that's going to be pushing it for me to reach the top with pot height considered. I might just put cement stones around the base to give me a few more inches of "reach".

I truly appreciate all the guidance for the experts.

I believe post #6 in the thread "Shapping a greenhouse JH Adriatic" should give you a good idea about pruning for a productive shape of the single trunk tree.

You're right Ottowan, Pete has several pictures that go with that one from a thread he did quite awhile ago. I had those all saved.