The development of a reliable subsoil model is crucial to optimize the results of the advanced (3 level) seismic microzonation. The definition of the model needs the contribution of distinct scientific skills (geologists, geophysicists, geotechnical engineers), that should interact, during the entire zonation process, to solve and reduce the complexity of the problem. This paper describes the methodology adopted in the recent experience of seismic microzonation studies carried out in Central Italy after the 2016 seismic sequence, addressing some critical aspects from the planning phase of the field investigation to the definition of the subsoil model for the numerical analyses. The interplay among different skills was crucial in identifying the subdivision of the cover units, especially when classification based on lithology and genesis was not consistent with the results of geophysical measurements.