In the framework of the EU Horizon 2020 McSAFE project, a Serpent2-SUBCHANFLOW coupling has been developed with the aim at performing large-scale pin-by-pin depletion and transient calculations in Light Water Reactors. While this tool is not tied to a specific type of geometry, a set of capabilities have been developed to generate the pin-level hexagonal models corresponding to VVER reactors. The handling of VVER geometries is based on the use of nested hexagonal regular meshes in Serpent2, pin-level subchannel models in SUBCHANFLOW and unstructured meshes for feedback exchange and interpolation. In this work, these features are explained in detail and illustrated in a VVER-1000 fuel assembly. For this test case, an in-depth analysis is made regarding the modelling considerations in SUBCHANFLOW and their impact on the neutronic solution. In particular, the use of coolant- and fuel-centered subchannels and the explicit modelling of stiffener plates is discussed.