Airframe flexibility effects have typically been captured by modal reduction of the airframe. Although efficient, this model may still be prohibitively expensive for preliminary design studies. This paper employs time- and frequency-domain system identification techniques to form a multi-objective optimization (MOO) problem to identify equivalent transfer functions representing airframe flexibility effects. Pareto-optimal sets are first identified for an equivalent transfer function of a force element between the landing gear (LG) attachment point and the center of gravity (CG) of a 150-passenger regional jet, and a second transfer function from the input LG force to the cockpit acceleration. The reduced models demonstrate the ability to generally capture flexibility effects with reduced computation times. The combination of time-domain and frequency-domain information ensures the positive time-history matches while the model remains physically realizable as it is rooted to frequency response obtained from the finite element model (FEM). It is hypothesized that this physical link allowed the model to be robust to the landing initial conditions.