The control of biochemical processes is a major goal in many fields, encompassing metabolic engineering and synthetic biology. Current approaches are based on ad-hoc designs, whereas a general and modular framework would be highly desirable, in order to exploit the well-assessed methods of control theory. The present work deals with the realization of an important component of control systems, namely the subtractor block. Adopting the framework of Chemical Reaction Networks (CRNs), a subtractor module whose output converges to the difference of the input molecular fluxes is devised. The convergence properties of the proposed CRN subtractor module are investigated via a singular perturbation approach. Finally, its effectiveness is investigated through numerical simulations and a comparison with an existing synthetic biomolecular circuit.