Self-assembled monolayers (SAMs) have received increasing attention since their introduction 30 years ago. Soon it was discovered that they can be used as alternative resist materials and are compatible with different established lithographic techniques commonly used in silicon semiconductor technology. Besides these possibilities to structure SAMs, other attractive properties emerged from the use of SAMs. E.g., the introduction of addressability into the patterns by selective functionalization with reactive precursor molecules and/or by applying suitable surface reactions was established. In this feature we highlight developments of photolithographic techniques that have been used in combination with SAMs serving either as resists for the patterning process or as precursor molecules for surface reactions, which can be performed on non-structured and mainly photochemically structured surfaces to obtain multifunctional surfaces with tunable surface properties. The aim is to provide an overview about the versatile possibilities to use silane based SAM systems to structure silicon-oxide substrates by introducing topographical as well as chemically heterogeneous surface structures. In particular the chemical activation of SAMs includes a large number of functionalization concepts which are intended to be summarized in this review. They will be introduced here according to the class of chemical reaction that has been used. Therefore, an introduction into the plethora of possible structures, which have been created by the combination of photolithographic structuring approaches, and the integration of tailor made surface functionalities into these systems will be highlighted. Additionally effective strategies to implement a diversity of chemical functionalities onto one substrate are summarized.