In this paper, the reliability of a finite element (FE) model including carbon-fibre reinforced plastics (CFRPs) is evaluated for a case of a complex thin-wall honeycomb structure designed for a scientific instrument, such as a calorimeter. Mechanical calculations were performed using FE models including CFRPs, which required a specific definition to describe the micro-mechanical behaviour of the orthotropic materials coupled to homogeneous ones. There are well-known commercial software packages used as powerful tools for analyzing structures; however, for complex (many-parts) structures, the models become largely time consuming for both definition and calculation, which limits the appropriate feedback for the structure's design. This study introduces a method to reduce a highly nonlinear model, including CFRPs, into a robust, simplified and realistic FE model capable of describing the deformations of the structure with known uncertainties. Therefore, to calculate the deviations of our model, displacement measurements in a reduced mechanical setup were performed, and then a variety of FE models were studied with the objective to find the simplest model with reliable results. The approach developed in this work leads to concluding that the deformations evaluated, including the uncertainties, were below the actual production tolerances, which makes the proposed model a successful tool for the designing process. Ultimately, this study serves as a future reference for complex projects requiring intensive mechanical evaluations for designing decisions.