A simplified asymmetric unit is proposed as a guide to optimize the internal arrangement of a membrane reactor with cooling tubes. This configuration is similar to a shell and tube heat exchanger, but some of the tubes are membranes. The internal layout has a lot of possible combinations, and its optimization could be considered as an art. A 3D model was developed by adapting a transient 2D model and was solved with Comsol Multiphysics 3.5a, a finite element software. Employing deforming mesh module of Comsol, the internal dimensions and meshing of the simplified unit were dynamically readjusted to allow the sensitivity analysis of one geometric design variable. Interpretation of the results provides good initial estimates on how many membrane and cooling tubes must be assayed so the number of configurations that need to be evaluated is reduced.