The deterministic transport code APOLLO3 R developed at CEA was used to setup the 2D and 3D neutronic models of the zero-power, water-moderated experimental reactor CROCUS, operated by Swiss Federal Institute of Technology in Lausanne, in order to verify the computational methodology and apply it to the interpretation of experiments conducted under the CORTEX European project related to neutron noise measurements in which CEA participates. The variants of the self-shielding calculation based on fine structure method were analysed and a fully heterogeneous 2D description of the reactor is tested with different discretisation options using the method of characteristics. The homogeneous model intended for the discrete ordinates, short characteristic calculation is also analysed with the emphasis on the production of equivalent cross sections. The reaction rates preserving equivalent cross sections are set on the basis of the whole 2D domain used as reference homogenisation problem.