tn the Database, under Tilesets, there's a setting for Priority. a Priority of - to 5 can be assigned to each separate tile. a priority of - means that it is beneath the player. a priority of 1 means that it is on the same level as the player; the lower half of the sprite will disappear underneath it, and the top half will appear above. a setting of 1 is best used for single-tile bits of scenery that you want the player to be able to walk both in front of and behind.
anything higher will appear above the player no matter what. a tile with a priority of 3 will appear above a tile with a priority of 2, and so on. tiles with the same priority will be layered based on what layers in the map editor they take up.
in the case of the trees, the tile at the base should be -, while the rest of the tree should be anywhere from 2 to 5 so that it appears above the player.