Don't specify a texture in the .fpe file and then copy the textures into the folder with the entity in it (in this case,a tree) after you build the game.
I am not sure if that is all there is to it but there have been several posts which give detailed instructions on how to do this.
Theoretically you could do this with any model if you gave it multiple textures...I think the model might have to be dynamic too.
Candles released a tree pack a while back that works and I believe they are Treemagik...his trees are guarenteed to work if you follow the instructions after you download it.
I know it for a fact because I beta tested it.