The control of chemical reactions has been a target for researchers since the development of lasers which operated on a timescale fast enough to follow nuclear motion. Since then a number of schemes have been developed, each proving successful in a selection of systems. In this paper we present results obtained following the implementation of local control theory together with the multi-configuration time dependent Hartree quantum dynamics algorithm, aiming to efficiently design control pulses for polyatomic systems. Control of multidimensional models of cyclobutadiene and pyrazine are presented and discussed. These results represent a starting point for further studies, showing the distinct advantages of using this approach for controlling chemical reactions.