I suppose you could use some low poly proxy objects for the trees and then use a pre-render MEL script to replace them with the real tree models at render time. When the render is over you could use a post-render MEL script to revert to the proxies. Of course this is a bit involved and troublesome but it works...

In addition you could put each tree in it's own render layer (not display layer) and render in passes using image format that supports alpha channels (such as maya iff, tif or tga) and then composite the resulting images in photoshop or some real compositing package like after effects...