When I collect wildflower seed, I always clean it to ensure successful storage and to show me just how much I have. To allow additional curing, I usually put off cleaning and processing the seed I collect until several weeks after I get it home. During this time, I store the seed in a cool, dry, well-ventilated place.
Separating the seed from the chaff is much easier when the seed is fully dry. Cleaning the seed will also flush out any insects. There are certain weevils associated with wild indigo (Baptisia australis and others), for example, that feed on the seeds. Although you don't have to remove the fluff from milkweeds, you gain more control over them and save on storage space if you do. My method is to hold the pod at the end opposite the stem, gently open the crease and pop the seeds off the fluff while holding the fluff firmly in place. Inevitably some fluff escapes, so this is a job best done outdoors.
The cleaning doesn't have to be perfect. I have had perfectly satisfactory results sowing black-eyed Susan (Rudbeckia hirta) seed mixed with chaff. Also, some seed doesn't require much cleaning. With prairie clover (Petalostemon spp.) and leadplant (Amorpha canescens) you need only yank the seed pods off their stalks. When pasqueflower seeds are ready they are easily detached from the heads. The seeds have long tails, but there's nothing to clean. After you have collected seed for a while you learn how to minimize the amount of chaff you bring home in the first place.
Excerpted from "Stalking Wild Seeds: Responsible collecting can enrich the garden with roadside flowers" by Ann B. Swengel, Horticulture September 1995.