few options ( but keep in mind that this problem exist with every scaning solution - laser, structured,photogrammetry ):
1. in PS 1.0.0 go to TOOLS - MESH - VIEW MESH STATISCTICS = FIX ERRORS, as i have discussed this part with agisoft it clean mesh for most errors, but its will be never perfect....
2. REPAIR in external app, like GEOMAGIC, XOR and etc. it better but still not perfect too :-)) sometimes it must repair 2-3 times before its good.
3. RETOPOLOGY in externall app( Zbrush, Mudbox, 3DS MAX, 3D COAT - automatic mode ) its best way but sometimes complicated, its about creating clean new mesh from the original scann data.
http://www.youtube.com/watch?v=qKTUIsPQ_uM 4. Printing solution - most of the 3D printer sw should be capable of repairing mesh ( STL repair ) at least Z-Corp have this option....