My idea is to place all trees at level , after we can save it to file. It will take a long time for big level.
==> Instead you can make your level's scaled top picture and draw your tree positions using some small shapes with different colors.

After you can make some functions which will determine tree positions (X,Y) from picture and also you should find Z poistions using TRACE function and write tree's (X,Y,Z) positions to INI file.