If you make a 3D object, then place it on your plant and realize that it is upside-down or inside-out, it means that you were pushing or pulling in the wrong direction when you dragged points in the Z dimension. Just return to the 3D object editor and reverse the Z values. The effect is something like this:

Before

After

To reverse the Z values in a 3D object in the 3D object editor,

       Click Reverse. You may not be able to see the effect if you dont have a rotated view of the 3D object showing; click Rotate mode and rotate the 3D object in one of the two View panels. Try reversing the triangles a few times and youll understand how it works.

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