The paper focuses on issues in experimental design for identification of nonlinear multivariable systems. Perturbation signal design is analyzed for a hybrid model structure consisting of linear and neural network structures. Input signals, designed to minimize the effects of nonlinearities during the linear model identification for the multivariable case, have been proposed and its properties have been theoretically established, The superiority of the proposed perturbation signal and the hybrid model has been demonstrated through extensive cross validations. The utility of the obtained models for control has also been proved through a case study involving MPC of a nonlinear multivariable neutralization plant.