Trees and flowers are different from props. You can save those together as a 3D Scene.
Unfortunately, I can't find anything in the manual, but I tried it out, and a 3D scene saves trees, flowers, and grasses, as well as terrains, the sky and any lights.
If you have props you want to save as well, you can temporarily convert them to terrain items. Right-click on a prop and select Convert to Terrain. Once the 3D Scene has been loaded, you can convert these sub-terrains back to props.