Historical ciphered manuscripts are documents that were typically used in sensitive communications within military and diplomatic contexts or among members of secret societies. These secret messages were concealed by inventing a method of writing employing symbols from diverse sources such as digits, alchemy signs and Latin or Greek characters. When studying a new, unseen cipher, the automatic search and grouping of ciphers with a similar alphabet can aid the scholar in its transcription and cryptanalysis because it indicates a probability that the underlying cipher is similar. In this study, we address this need by proposing the CSI metric, a novel way of comparing pairs of ciphered documents. We assess their effectiveness in an unsupervised clustering scenario utilising visual features, including SIFT, pre-trained learnt embeddings, and OCR descriptors.