This talk will give an overview of well-established tools like Unicode, XML and TEI and less known ones, like Omega, applied to the preparation (and further transformation into books, online publications, etc.) of scholarly documents, in particular those involving scholarly languages: Greek, Hebrew, Arabic, Syriac, etc. We will study (and give concrete examples of) different cases, ranging from simple texts to dictionaries, parallel texts, critical editions. In each case and for each language we will discuss the encoding and structure involved, as well as the necessary linguistic transformations like uppercasing and hyphenation, and different strata of the document like accents, short vowels, diacritics, editorial marks, etc. In particular we will discuss grammatical phenomena like the hamza rules in Arabic or the subscript iota in Greek and the choices they involve. Finally we will introduce typographical typesetting like yet another transformation of the document, and will discuss issues of macro- and micro-typography related to language and script properties. Our aim is to show how encoding, structuring, typesetting and linguistic transformations are intimately related to each other, illustrated by concrete examples in the above mentioned tools.