A witchhunt refers to methodology for identifying and accusing criminals then further exposing the conspiracy surrounding the presumed criminal activities of the criminals' web of friends and relations. This method of investigation is now virtually discredited. Historically, it referred to accusations of someone being a witch and deducing that family and friends were likely witches as well. Today, the term witchhunt is most often used as an accusation against overly zealous prosecutorial procedures.
Historically, the term describes the investigative procedures used during witchhunts of the Middle Ages up until the early Colonial period, during a time when investigators were earnestly hunting for witches. At the time it was believed that witches were blasphemers who worshiped Satan or other occult figures. It was further believe that through their occult practices witches brought hardship to the community at large and endangered the immortal souls of unwary Christians. The most recent witchhunt in recorded history is the Salem Witch Hunt. The crime of witchcraft was punishable by death by fire. It was presumed at the time that witches were highly motivated to hide their true nature (not because of the penalty of the crime but because of the evilness of their practices). Therefore, certain investigators or inquisitors, often acting under the authority of the church, would investigate and prosecute this crime when a web of witches was suspected.
An investigation would usually start after the identification of a problem which the community believed might have been caused by witchcraft. For example, a disappointing crop, a cow that did not give milk or a barren female were all prime causes for suspicion. The investigator had little to go on when trying to connect a cow to a witch, but he would often begin by questioning anyone who might know of any witches. If a member of the community or a child suspected witchcraft in a particular individual that individual would immediately be apprehended. Through a mixture of coercion and torture the witchhunter would not only extract a confession from the detainee, but also the names of associates who were allegedly similarly involved in blasphemous acts. In this way, the inquisitor could start with the flimsiest of evidence and through this "investigative process" identify a conspiratorial web of witches and blasphemers. 
Modern witchhunts usually describe a situation where a prosecutor or special prosecutor begins deposing targets to uncover a web of defendants. Rather than investigating a specific occurrence of a crime, a witchhunt focuses on individuals, presumably suspects. Rarely such investigations are used to bring down real, but elusive criminals, such as Al Capone.  More often witchhunts are political weapons which hope to ensnare victims in trumped-up perjury charges or perhaps trick victims into revealing crimes involving friends or relations.