Try to keep your coop in a level or human leveled area. An area that won't flood or hold water after a big rain or is too close to the neighbors are big considerations. If you will be letting your chicken free range keeping close to the woods is a good idea to protect the birds from flying predators, but also provides a area for hawks to sit on limbs and watch your chickens so keeping the woods natural with deadfalls and brush for your birds to get under will help protect them, A clean forest floor won't protect them from airborne predators.
Personally I would want to coop adjacent to the woods not in it just so I wouldn't have to remove trees, stumps, etc. However with a little creativity you could build a coop using lives trees for supports kind of like a treehouse. It also depends on the type of trees the woods host. In Nebraska we have a lot of Chinese Elm that die young and always have limbs falling, These limbs can rain havoc on a run or even the coop. If your woods is mostly hardwoods like oak or maple that would be better. Long lived pines like white or red pine or douglas fir or spruce would also be okay, but white or red cedar or jackpine wouldn't be good. Also trees like Chinese Elm and many fruit trees will spot rot where a branch fell off, These areas can easily be hollowed out by racoons or other critter to be used for homes. In these cases you are putting food in the predators kitchen so to speak.
