Often a Witch-Hunt targetted people based purely on rumour or superstition and once they became convinced of a victim's guilt they would engage in torture, harassment and even lynching - one of the most well-known of the Witch-Hunt punishments was to be burnt at The Stake (although this was actually very rarely used).
Many people lost their lives to the Witch-Hunt in the past (mostly women, though more men than its normally stated met a similiar fate) - either being hanged, groatted, beheaded, burned at The Stake, tortured to death or drowned via the Dunking-Stool. The horrific and unfair nature of the Witch-Hunt continues to live on in infamy and has been adopted for any situation that is seen as being akin to it, such as when governments or a group of people pursue percieved enemies with reckless abandon.
Despite popular belief, witch hunts actually had very little to do with religious beliefs. During the Middle ages the Catholic church openly critized belief in witches denouncing it as heretical to belive such a power other than God could exist and would only exercute people during times of mass panic purely to quell the population. It wasn't untill the early modern period, when the Church had lost much of its power due to the rise of Protestantism and the increase of power in the government, that Witch hunts became popular. Normally for political and social reasons. Although originally supportive of the Witch-Hunt most religious societies and governments have since gone on to condemn the actions of their ancestors and pardoned most of the victims who died as a result of these events.