Leading attractions including Falkland Palace and Culross, in Fife, Brodick Castle, on the Isle of Arran, the birthplaces of Robert Burns and JM Barrie, and Newhailes House, in East Lothian, are among 39 locations named.
Brodie Castle, in Moray, Culzean Castle in Ayrshire, Fyvie Castle, in Aberdeenshire, the House of Dun, in Melrose, and the House of Binns, in Linlithgow, are among the other sites identified by historian Dr Ciaran Jones.
His research, which focuses on the period between the passing of Scotland' s Witchcraft Act in 1563 and its repeal in 1736, recalls how how witch hunts “came in waves and intensity” which were focused in the Lothians, parts of Fife, Aberdeenshire, Stirlingshire and other parts of central Scotland.
However, the islands of Canna, Iona, St Kilda, and Unst and Yell on Shetland are also identified.
The research explores why 85 per cent of the 4,000 people accused of witchcraft in Scotland were middle-aged women.
Dr Jones states: “Women were generally seen as more quarrelsome and were thought to resolve conflicts using words rather than physical violence.
"This idea that women were more likely to use words than men during confrontations made them more susceptible to witchcraft accusations, since, after all, witchcraft was also about the power of the spoken word.
"The Kirk in Scotland was also extremely concerned with femininity and, in particular, sexual crimes such as adultery and fornication.
"Women tended to be the focus of the Kirk’s discipline, mainly because it was easier to prove through pregnancy if a woman had committed such crimes. Transgressive women who shattered the ideal of the good and godly wife could find themselves more likely to be accused of witchcraft.
“It was also believed that witches were more likely to be women because of the stereotypical and misogynist view prevalent at the time that women were more easily seduced by the Devil.”
The report explains how witch-hunters were “usually men of some renown and standing”, including ministers and lairds, who were often ideologically motivated or sought to profit from their involvement.
Religious rhetoric was said to help provide justification for the hunting of witches considered to be “enemies of God and a threat to Christian communities”.
The report states: “Powerful and local individuals in the communities where accusations surfaced, and where most witch trials were conducted, had vested interests and exploited opportunities for witch-hunting.”
The research also recalls how methods of torture, including sleep deprivation, were used to extract confessions, with interrogators regularly securing the names of others who would go on to be accused.
The research was commissioned last year by NTS following an outcry over plans to name a new holiday apartment in a 500-year-old Edinburgh townhouse after a minister linked to the persecution of witches.
In its introduction to the research, NTS states: “These stories are a rich insight into the social and cultural world of early modern Scotland, stories that we naturally want to share with our visitors.
"But this is also a complex and challenging history, with difficult themes of violence and injustice, which make it all the more important that we tell these stories accurately and with sensitivity.”