This paper describes the full procedure adopted in the context of the Clavius on the Web project, which aims to help Web users to appraise the importance of specific manuscripts by going beyond their digital reproduction. The proposed approach is based on the multilayered explication of linguistic, lexical and semantic data representing the innermost nature of the analyzed manuscripts. The final purpose of the project is to gather and display the results of the three layers of analysis through interactive visualization techniques and export them as Linked Data. All the analyses rely on the XML/TEI encoding of the text, followed by a CTS-based tokenization. As a working example for this paper, the analysis of a portion of a manuscript provided by Historical Archives of the Pontifical Gregorian University will be illustrated. The text is a letter written in Latin and sent by Botvitus Nericius to Christophorus Clavius in 1598 from Madrid.