It depends greatly on the operator if you want this to be a success. Some operators have a CLEAR EVERYTHING, anything left is an inconvenience to me mentality. You'd best ask around to see who has done what with what results before turning a machine loose on your property.
Some of those guys are fantastic, some are not. Some you can't talk to about anything they are all "yeah, yeah" and won't even shut the machine off if you have a question. (for sure BE THERE when work is being done).
I say this as a veteran of both disasters and successes /w3tcompact/icons/mad.gif + /w3tcompact/icons/smile.gif.
If you are planning on leaving a tree, and you want the tree to survive, have the operator stay outward the "drip" line of the tree. With most trees the roots match the branch spread, if rain can drip off the tree, there's probably a root nearby.
I say this as although cutting the tips off some small roots is not a disaster, when they are clearing with the clearing rake down in the ground, they can catch a root and tear the entire thing off back to the stem of the tree.
Each tree is sensitive to one degree or another about the level of the root in the ground. If dirt is removed off of the root system, or piled on it, it can affect things adversly. Try to leave things as they were as each tree has it's own comfort level (determines the roots need for oxygen vs moisture)
Doing this has a drawback, that being it takes longer to get the work done, if the guy has to turn the machine around and gently back drag some brush, and constantly have to think about what he is doing time is lost. I would find a guy you can talk to and let him know you aren't one of these guys that wants a CLEAR IT IN XXX HOURS and stands there with a stop watch or refuses to pay if it takes longer. Sooner or later you'll find a good operator who does clearing, but also has done landscaping for nurseries and builders who build houses with mature trees, those are the guys to grab.
Some guys don't know where there machine is and don't care if they back up to and knock the bark off a tree. A tree can be greatly stressed or even killed depending on the damage to the bark. I was trying a guy out once, went through the drill, the first thing he did was dig up a big stump and then ram it into another tree I wanted to keep. "OK, thank you very much, bye"
You can band the trees, but it will help the operator and you if you band the root area you also want to protect. And put the flags on brush or on sticks high enough for him to see them.
It's so easy to go back later if you want to add to what's removed, and so impossible to undo a disaster.
I find it easier to do clearing with an excavator (or my backhoe) as you can rake the ground with great care, and clean up your mess when done. I was pretty good at not damaging things my first day on a 28,000 pound machine. (except for my own ego and adrenalin glands, but that's another story I've already told! /w3tcompact/icons/shocked.gif)
A new neighbor bought a place up the road and was trying to remove years and years of neglect (massive blackberry vines) over what was previously obviously someone's extensive planting of different shrubs etc.
He was doing it with clippers and having a time of it, when I saw it I drove the tractor down. He was friendly but was terribly afraid I would demolish what he was trying to do. I said I'll go slow and if at any time he says stop, I'll stop. With the backhoe idling I just reached around using the backhoe as my "hand" and pulled the vines out. the blackberry vines are so tuff that after I pulled them out, going carefully around the trees and shrubs I was able to pull out 20-30 foot long vines in to a nice pile we could deal with.
Backhoes make good gentle "weed" machines!