Where the decision has been made to remove trees from sensitive sites, they are usually felled and the stumps left in situ, thus minimising below ground disturbance. The remaining stump and root system can still produce growth long after the stem has been removed. Many tree species (especially hardwoods) are renowned for their ability to produce new vegetative growth (coppice shoots), but this differs with tree age and species. As any regrowth will ensure the continued growth of the root system, fresh stumps may be given an application of herbicide. The practicality of this process may be limited, as herbicide is often only translocated a short distance into the stump and its application may be environmentally undesirable.
Where plenty of notice is possible prior to felling, a process known as "ring barking" may be employed. This prevents newly synthesised nutrients from being stored in the roots and those present become depleted. The tree can subsequently be felled with little chance of either coppice or sucker growth.
Once severed from the stem, roots will be subject to attack from soil micro-organisms, resulting in the eventual loss of root integrity. Once decayed, voids are left within the soil. Water can drain through these channels and the surrounding soil and will creep in from the sides. Any organic material derived from the root itself may be mixed with the soil by bioturbation. Such voids may cause problems where movement of soils, deposits and artefacts occur, thus confusing the stratigraphic interpretation and archaeological context.
The removal of trees from within an area of woodland can put adjacent trees at risk from windthrow. At particular risk are dense upland conifer plantations, often grown on poor or thin soils producing trees with potentially shallow root systems. If areas within such forests are opened up to expose archaeological sites, the trees on the newly created edges are at risk of windthrow due to poorly developed root system and a sudden increase in exposure. Such implications must be considered prior to opening an archaeological site within any woodland.