When you siphon your beer off of the trub to either a secondary clearing tank, or to the bottling bucket, just hold the racking cane above all the junk. Since you can't really see it at first, I just put the racking cane a little under the surface, and lower it as the beer level lowers. That keeps it above all the trub and you siphon clear beer off.
Broken Leg Brewery
Giving beer a leg to stand on since 2006