Just throw them somewhere outside the radius of a workbench and they'll despawn eventually.

Though I find the best way to not end up with tons of junk is to not pick up everything you see. I keep one stack of each material at max (except building, food materials etc.) because the probability of me needing more than 50 leather scraps is highly unlikely. Trophies, I only keep one of each just for the sake of collecting them.