Unfortunately, a number of Detros' recommendations aren't that good:
- Detros is slightly wrong in details when it comes to using a ballista: the tree isn't turned into a pile of matches, but is disintegrated totally (including leaving a hole in the water where the tree stood. That hole is filled up if waves are created).
- Causing a cave-in on top of a tree does NOT work. The cave-in will be suspended by the smallest twig of the tree, rather than smash it.
- Reachable branch tiles above water works if the tree is a kind that has reachable branches (some do, some don't). There is also a risk of the wood cutter getting killed in the process by being swept into the water by the splash of the logs.
- Magma doesn't work. Cave trees can grow in magma, and if you pour magma on top of them you can start a fire that will burn the twigs and can set fire to the cave moss, but the trunk remain unaffected. I've heard fires can occasionally destroy a (surface) tree, but I've never seen it myself.
A lake without edge contact can be drained, as Detros said. The easiest way is to dig a tunnel to the edge, carve a fortification in the edge, and then channel down so the lake drains into the tunnel. Magma doesn't work that well for the complete process, because you can't reach the water underneath the tree's branches. You can, of course, obsidianize everything around it and then channel the obsidian so the water can pour out, spread, and evaporate, though.
My primary solution is disintegration through ballista. When the blocking trees are out of the way I can then proceed to obsidianize the submerged cavern entrances (my main reason for wanting to get rid of trees in water. The other one is to dislodge campers, but they tend to just move to another tree).