The usual way a person was determined to be a Witch in Elizabethan England, was through confession. Unlike most of Europe at the time, torture was outlawed in England, so other pressures were brought into play, such as social or economic.
If you read the article here on CyberWitchcraft, you'll find that most who admitted to being Witches were not killed. Only those who continued to deny their involvement, tended to be put to death. Most would admit to being a Witch and take a lesser punishment.
Evidence of Witchcraft was usually gathered by physical examination. Moles, birthmarks, or deformity was considered a "Devil's Mark" and used as evidence that the person had made a deal with the Devil.
