The present invention provides methods and systems that are helpful for authenticating or protecting physical and electronic documents like financial documents and identification documents. One claim recites a method including: receiving digital data corresponding to a physical document; transforming the digital data into a frequency domain; comparing characteristics associated with the transformed digital data to predetermined characteristics that are associated with a first document type, and if the characteristics coincide, determining that the physical document is of the first document type; and if the characteristics do not coincide, comparing the characteristics of the transformed digital data to predetermined characteristics that are associated with a second document type, and if the characteristics coincide, determining that the physical document is of the second document type. Of course, other claims and combinations are provided as well.