As far as what you have depicted, I would suggest collapsing the final node options, the same way it seems you have collapsed the options for the Tree and the Branch. Once a user makes a selection, there is no need to show the other options. This would clean things up a bit with your current design. (Assuming they do not need to rapidly switch back and forth at the leaf level).
Also, if there are multiple rows of Tree->Branch->Leaf selections, you could possibly keep the rows below the first (or current) one collapsed until the that row is completely selected. This would reduce the information noise on the page and help walk the user through each T->B->L selection set.
You may consider breaking apart each row into separate screens, almost like a wizard. Having too many selections on a single screen can potentially get overwhelming. Assuming of course you have the freedom to split them up in this way. Careful though, as this could slow down expert users if they prefer the shotgun approach. (Maybe have an "Expert Mode"?)
If you have active or potential users, you can always ask them for feedback. Sometimes they can provide key points of insight that will help you better understand their needs and their perceptions of how the tool should work. Always understand who your users are.
Hope this helps some.