Implicit complexes (ICs) provide a novel framework that makes it possible to model heterogeneous objects exploiting hybrid representation schemes. The paper is focused on the application of IC based heterogeneous models to designing data processing tools for finite element/finite difference (FE/FD) analysis. We give a brief description for implicit complexes, their structure, basic operations and implementation. Then we represent our approach to designing FE data structures within the IC framework. As an example we consider software architecture of a radiative magneto-hydrodynamics simulation code MARPLE developed in IMM RAS for numerical solution of research problems in the field of gas-dynamics and plasma-dynamics.