Matthew 3:11-12 I indeed baptize you with water unto repentance: but he that cometh after me is mightier than I, whose shoes I am not worthy to bear: he shall baptize you with the Holy Ghost, and with fire: 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.
When John the Baptist used this reference in Matthew 3:12 he was referring to a very common practice that was used in the harvesting of the wheat to separate the wheat from the chaff. When the grain was harvested it was tossed into the air with a winnowing fork and the chaff which was light would be carried by the wind but the kernels of grain which was heavier would drop much closer. The grain could be then gathered into a small basked and the process could be taken to the next step of further refinement and separation. This is what is referenced as thoroughly purging the floor or gathering all of the grain for storage. When the grain had been gathered and safely stored then the chaff would be piled up and burned as it was of no further use. While the grain was growing the chaff served the purpose of protecting the grain but once the grain was ripe it lost its use.
So now we come to our question, what is the illustration of winnowing pointing out? John the Baptist pointed out that he was baptizing with water but Jesus would baptize with the Holy Ghost and with fire. Most of the time when we reference baptism it is in reference to water baptism which is the picturing of the death, burial and resurrection of Jesus Christ. It is also a picture of the testimony of the new believer who has died to sin, been buried in a grave of water and raised to walk in newness of life.
Now lets look at the baptism of the Holy Spirit. There is some confusion on this with some Christians. Ephesians 4:5 One Lord, one faith, one baptism, Their understanding is that you get saved and then there is a second work of God that they identify as the baptism of the Holy Spirit. This is not sound doctrine as the Bible teaches that you receive the Holy Spirit when you believe or are saved. It is further emphasized in Eph 4:5 where the Greek translates it as one placing into. It is the same as the sealing of the Holy Spirit and it is our earnest or down payment on His promise of eternal life. This is to be differentiated from a filling of the Holy Spirit or being controlled by the Spirit. The Holy Spirit is sealed with our spirit in an irreversible act that will stand the test of time and fire. The purpose is to free us from sin and to transform us into creatures of righteousness. It is a process that continues until we are caught up to meet the Lord in the air. As the grain is what is valuable in the harvest, so also is the believer who God will so equip with the Holy Spirit so as to enable us to stand the test of fire. Our works will be burnt up but the work that the Lord has done on us to separate us from sin, just as the grain is separated from the chaff, is what is valuable to God.
The baptism of fire is another vivid illustration and can be understood as we look at the life of the believer. Once he has become a Christian, the Lord goes to work in His transforming process. He allows trials and tribulations and persecutions to come on the believer and is often accused of not caring for him. These events, though hard to experience, are designed of God to teach us eternal truth. He said that if they persecuted Him then they will persecute us. All our works will be burnt up but that which is eternal that has been built into us will endure and fire will have no effect on it. Things like the fruit of the Spirit (love, joy, peace, long suffering, gentleness, goodness, faith, meekness and self control) is being built into us and will remain through the fire. It is all to change our thinking so that His ways become our ways and His thoughts become our thoughts. Then we will understand.