The trees are made of blocks.
Each block must fit in a cube the same as any other stonesense tile.
If the trees were all one picture, intersecting buildings would not be able to "cut off the branches that are in the way", treetops would appear to stick out at odd angles should a floor cover them, and all floor/wall tiles drawn after the tree would be drawn over the top.(I believe stonesense draws top to right, moving towards the bottom left, then stacking levels.)
The trunk is a single tile, all other parts fit around that. Though you can half fill a tile on either side so the tree is only 2 wide/deep, it would actually use 3 wide/deep tiles.
Trees should be in .png arrangement can be defined in xml.
I drew mine and chopped later. It's a lot more work to fill in the parts that are only seen as layers are chopped.
If it helps, here are the trees without leaves, if you want them as a starting point or guide, go for it.
start counting at 0, 0 is center, 1-8 run clockwise from the top, 10-18 is the next level, 9/19 indicate a layer to be inserted(9=between 0-8 & 10-18; 19=on top).
I hope someone can get through all the trees, I focused so much on how they looked on their own that I forgot to check how it looked in stonesense. Now I'll probably have to start over with most of them.
EDIT:Oh, and on the hide treetops thing, I believe the treetops are cut off the same as any constuction once you move the view lower than the top. (another reason why they are sliced up into cube volumes)