simulating an imported mesh (from matlab)

Hi,
I'm trying to simulate a prescribed displacement (one end is fixed and the other one displaced) of a mesh created in matlab (the geometry is from a microCT image). The problem is comsol dons't recognize the different surfaces. I used the box option in the mesh, but then the displacement is all messed up.
anyone has an experience with an imported mesh?
Thanks,
Shira