As of mid November is was pretty clean.  One easy step-around (logs) in the upper just above the lead in to Shark's Fin is all I remember.  Of course, that was 3 months ago... 

upper will likely be low by the weekend. the lower may be a better bet.

We ran lower Matheny twice on Monday with the Quests at 13k and dropping , was a nice medium low flow, water was just comeing over the rock upstream of the bridge. The lower is totally clean. I haven't been in the upper this season yet.   But if you do head out to Matheny for some low flows this weekend don't forget about the lower, it has 2 great canyons and has way more rapids than the middle.   Many people pass up the lower thinking it must be more mellow then the middle, but it's not.    Running Matheny top to bottom is an amazing day. I like around 7k to 12k on the Quests for the upper (any higher and shark fin starts to get really sticky).   For the lower I like 12k to 50k on the Quests, it can be run much lower but it gets boney.   High flows on the lower is quality, clean, big rapids, one of my favorite runs.
I bet there is snow near the top of the road to the upper this weekend, also always bring a saw in the car, I almost always have to cut a tree out of the road when I go to Matheny.