Runes are the elvin alphabet. It consists of two main orthographies: a formal version and a simplified version. The formal version uses the elves' ancient alphabet that has special flourishes to make it look sumptuous. The formal orthography has fallen from mainstream use and is only used for formalities. In most cases, the simpler orthography is used. Special Cipher Runes may also be used for classified documents; these special runes can only be read by individuals who had the cipher implanted within their minds. The Black Swan and the Council make use of this, it can be presumed that the Neverseen do as well. Reading elvin Runes is instinctive for elves, who have an inherent ability to speak the Enlightened Language at birth and understand both orthographies of elvin runes.
Sophie is the only elf incapable of reading the formal orthography; she is only capable of reading the simplified orthography and the Cipher Runes implanted within her brain by the Black Swan. Reading elvin runes should be instinctive for elves, the way speaking the Enlightened Language is, but for an unknown reason she cannot read it.
There are also ancient runes, which even Mr. Forkle had trouble deciphering. They are known to have extra curls and flourishes.
Lexicons are used to translate runes.