Matthew 3:12 Whose fan [is] in his hand, and he will throughly purge his floor, and gather his wheat into the garner; but he will burn up the chaff with unquenchable fire.

This passage refers to a winnowing fan, shovel, or fork and a threshing floor. It does not matter which type of winnowing tool is used, or which method of threshing is employed, because they are all used to accomplish the same task. When harvest time has come, the wheat is harvested and removed from the field. It is gathered together into one place to be threshed.

In this parable, we are given one particular type of plant, from which two different products are produced. Take note of this very important understanding and the fact that both grain and chaff are derived from the same stalk of wheat. These stalks of wheat are gathered together and threshed. Threshing is a process of beating or crushing. There are several methods that can be employed to accomplish this task, including the use of animals to trample the stalks. The purpose of threshing is to separate, or free, the grain from its covering.

The chaff is made up of the empty seed coverings and broken bits of straw that accumulate during the threshing process. As noted above, both the grain and the chaff are derived from the same stalk of wheat. Once the stalks have been properly threshed, the process of winnowing begins. First, the large stalks which remain are removed. At this point only the grain and chaff remain.Winnowing is the process of lifting that which remains into the air and allowing the heavier grain to drop to the ground while the air carries the lighter chaff away. Eventually this process separates the chaff from the grain.

The grain is then placed into a garner for safe keeping and the chaff disposed of. One must keep in mind that we are dealing strictly with one type of plant, commonly wheat, and that both the grain and the chaff are parts of the same plant. Both are derived from the same kernel of grain, the chaff which is the seed covering, and the grain which is the meat or fruit, hidden within, or incapsulated by the chaff. The regenerate child of God will produce either grain and/or chaff. The chaff must be loosed so that the fruit within can be released.

His winnowing shovel is ready, He will cleanse thoroughly His floor where He has collected His wheat for threshing. He will gather the grain thereof for safe keeping, but will consume with fire the chaff thereof with inextinguishable fire.

The above is my personal translation of this passage, without adding to or taking away from. It allows for better understanding of what is said. Notice that “He will cleanse thoroughly His floor”. The wheat is gathered on the floor. It is not just the chaff that He will clean from the floor, but everything. There will be nothing left on the floor when He is done. The wheat has been collected for threshing, to seperate the grain from the chaff. The wheat are His children, and the threshing of the wheat is the chastening of His children.

Related passages:
Matthew 3:10-11
John 15:6
1 Corinthians 3:13 & 15
Hebrews 12:29
1 Peter 1:7