I cut the trunk off flush, drill a hole in the layout, and glue it in. If the trunk is too short, I drill a small hole in trunk and a dowel of the right length and use a wire in the holes to add the dowel and lengthen the turnk, then insert it in the hole.
Putting trees in gets boring in ahurry, too. It is simply amazing how you can have so many trees and it does not look like nearly enough. There are about 400 trees in this end of the layout (about half is shown here) and it really needs about couple of hundred to look like a real forest.