There are 2 ways, if they are in a forest where it is more appropriate to fake the shadow of the forest not individual trees, use a clip brush that is slightly (2/3 units) larger than the entity marker, not flush to the floor, and is tall enough so you cant jump on top of it. That works pretty well for me, however, you can shoot through the trunks, so they won't provide any cover.
The second way is to do the same with a brush and then select the 'no draw' flag on the surface menu (press s, click no draw box). This is probably the best way as it casts a shadow of the trunk and can't be shot through, but you'll have to remember to make the whole silhouette of the tree when you make this method or the shadow of the tree will just look like a stick in the ground.
- Dag
edit: curse you, Laged!