The grain was either raked with a “winnowing fork” or thrown into the air where the breeze would blow away the chaff but not the heavier grain.
Similar agricultural methods are still used in the 21st century in the Near East, Africa and Asia, and the process can be traced back to several ancient cultures, including Greece and China. Sometimes water is used (instead of wind) to separate the chaff.
The image of winnowing occurs several times in the Old Testament, symbolizing the dispersion of Israel during the exile. It is also used as a metaphor for the judgment of Yahweh.
In the New Testament, which for most Christians fulfills the Old Testament, the image of winnowing designates a final judgment and eternal separation of good souls that enter heaven, vs. evil souls that descend to hell.
Along these lines, John the Baptist awaits the Messiah (Jesus) who holds a winnowing fork (or fan) to clean the threshing floor, gather the good wheat and throw the useless chaff into the eternal fires of hell.
His winnowing fork is in His hand, and He will thoroughly clear His threshing floor; and He will gather His wheat into the barn, but He will burn up the chaff with unquenchable fire.” – Luke 3:17
Catholic teaching has, to some degree, elaborated on this ancient, polarized view of salvation vs. damnation with the idea of purgatory.