It seemingly does this nicely, but in fact what it does is just rotate the imported prefab so that it looks like it’s up. If you rely on anything that references the mesh directly - it’s 90 degrees the wrong way. So my custom trees are apparently all lying on the ground!
Is there any way around this other than modeling…sideways?
Hi, some people work around this problem by creating an empty game object, and making it a parent of the gameobject you wish to rotate. Then apply the rotation to the top game object.
Then, create a new prefab based on it, and you should be hunky dory. It’s kind of a hack, but it might suit your situation. 
This works for a prefab, but not for a mesh! The mesh remains 90 degrees the wrong way, and thus using them as trees leaves them lying on the ground 
what 3d program are you using? If it is max then you could under the Hierachy tab rotate the pivot, with “Affect Pivot Only” on.
In most other programs, you can just select all the polygons for the model and rotate them to where you want them.
Rotating it while the polygons aren’t selected just changes its rotation like how Unity would do it.
Hey
I found this in the External Tools FAQ
http://forum.unity3d.com/viewtopic.php?t=11004
Happy Easter Bunny!
Yes, I met the same problem.