Hi! I had same problems with my clouds. What i tried, was exporting these clouds to cloud compare (free software
). There you can run some noise filter under : Tools-> Clean. After getting a hopefully cleaner dense cloud, i was creating a mesh in cloudcompare and then reimporting this mesh to agisoft for DEM generation, because Agisoft is not able to import dense clouds.
Maybe this helps!
Greetings toffersan