Shaping the canal system to promote disinfection and obturation is the cornerstone of molar root canal treatment. Clinical outcomes, both long and short term, hinge on the technical quality and attention to detail invested in this step. Moreover, biologic outcomes such as apical bone fill are mainly dependent on antimicrobial efficiency and retention outcomes are enhanced through dentin preservation. This chapter summarises the currently understood best practices for shaping, disinfection and obturation, independent of specific instruments or technologies. The historically proven lead principle is here, as in medicine in general, ‘do not harm’. Building on other chapters in this book, the rationale and literature supporting the must-haves and must-dos to fulfil the objectives for pertinent steps of shaping, cleaning and filling during root canal treatment are described, along with the underlying rationale.