Tommy,
I think you have a very idealistic view of saving natural landforms! It is so common to clear trees that we expect to have to smooth things back, perhaps adding topsoil to fill ruts, etc. and that is if there is no planned grading in the areas where the trees were removed. To answer Drew, I don't think there is any density of trees that would prohibit clearing technically. I am sure there can and are protests about the overall environmental desirability to do so, but that is a different story.
Lou,
We normally specify that cleared trees are put in pits in out of play areas. They don't usually settle a lot, but over time, they settle a little, so you don't want them under tees, greens or irrigation lines. You may recall the little water fall at Tempest behind the 10th green. When we dug out to clean that up, it turns out that the dam and road were built right over clearing piles. It's a wonder the whole thing hasn't collapsed over the years.
We generally build a small (or big, depending) mound over the clearing pits just in case, since level would eventually create small pockets. We also require the clearing contractor to clean up side branches, and stack the logs criss cross in layers, pushing debris in the voids. The basic idea is to compact the material as much as possible to reduce settling.
On a fully wooded, 18 hole site, it is sometimes difficult to find an area to do all that!
We also find the biggest issue can be the brushing (i.e., removing the small trees and shrubs under trees to remain). It's hard to do, usually mechanically with a track hoe reaching as far as possible in the trees. Topsoil replacement is usually necessary there, and fine grading often has to be done by hand. For cost reasons, it's often omitted from the contractor's work, figuring the superintendent can do it as winter work. That rarely happens, as they forget about it. Over time, those area grow back, encroach, etc., all while causing lost golf balls the entire time.
Drew,
As Tom Doak mentioned, when you cut the logs off, removing the rest of the stump can be more difficult. In reality, it's one of those things that sounds better to clients (yah, we make money off of trees!) than it really is. Often, contractors bid the same amount for clearing and burying as they do for harvesting timber and then clearing stumps. While it's more sustainable, it is also more time consuming and construction personnel are almost always more worried about their schedule than some big picture notion of saving the trees.
Another problem with tree harvesting? The harvesters usually want to take the big trees you want to save most! I find they have a few intentionally accidental "oops" per project for that reason, LOL.