The Observatory of the Vadose Zone (OZNS) is addressing the role of the unsaturated zone in the transfers of water, heat, and pollutant, between the soil and the aquifer. This project implements a unique observatory within the Beauce Limestone Formation at Villamblain (France). This observatory consists of a large central well (20 m deep and with a diameter of 6.1 m) surrounded by satellite drill holes and surface installations within an area with a radius of a few tens of meters. The overall observatory spans from the surface down to 25 m depth, reaching the aquifer and the barrier layer of the Molasses du Gâtinais. The instrumented surface, central well, and satellite drill holes will produce decade-long records of the vadose zone to evaluate its impact on water and pollutant transfers, while monitoring its long-term evolution in a context of climate change. The large central well is primarily designed for easily installing, maintaining, and testing geophysical and hydrological sensors over the lifetime of the observatory, but it also provides a unique chance to observe the complex structuration of the vadose zone and its host. In particular, the scale and configurations of the site provide a unique view of these rocks. They are made accessible at a micro-to-decametric scale, which extends drill core observations, and provide a nearly 3D view. This is interesting by comparison with typical outcrops at that scale (e.g., quarries), which are mostly 2D. Preliminary observations, from surrounding drill cores, revealed a particularly complex limestone formation, which consists of a series of terrestrial limestones, with palustrine and lacustrine facies and breccias, affected by a long history of fractures and alterations, silicification, and karstification. A very detailed characterisation of these facies thus requires to provide a high-resolution context for the various measurements and simulations of the transfers in the vadose zone.This contribution presents the construction of the numerical architecture and the acquisition process implemented for accommodating the very restricted access to direct observations during the construction of the well, which encompasses laser scanning (lidar) and high-resolution photogrammetry. The implications of the different acquisition protocols implemented during the process are discussed in terms of impacts on resolution, coverage, and spatial accuracy. The scanning was performed through 14 distinct stages, where only around 1.5 m height was accessible each time. One of the challenges was thus to stitch the different model rings into a common model. In the end, a complete model of the well surface was recorded with an average resolution of 3 pixels per millimetre.