A recently developed methodology for aircraft structural design, based on nonlinear airloads, is extended to include a modal-based optimization option and is employed with a new computational aerodynamics code for loads analysis. Nonlinear maneuver loads are evaluated by a computational scheme that efficiently combines fluid dynamics iterations with iterations for elastic shape deformations and trim corrections. An efficient design process is obtained by performing several structural optimization runs during one maneuver load analysis, where each optimization is based on the interim nonconverged airloads. To allow for the efficient application of the method with large finite element structural models and many constraints, the discrete-coordinate optimization scheme is replaced by a modal-based optimization where a set of low-frequency vibration modes of the baseline structure is used to represent the structure throughout the optimization, both for response analysis and for sensitivity analysis. Comparative modal-based and discrete-coordinate design cases are shown to converge to the same optimal design variable values, even though they do not follow the same path. Two flow solvers are used, one of which is a newly developed Euler/Navier-Stokes computational aerodynamics code that is capable of handling complex geometries by using the Chimera overset grid method. The method avoids the problem of mesh discontinuities due to elastic shape deformations and control surface deflections because the displacements of each component affect only the component's mesh. The method is demonstrated with a wing-fuselage-elevator transport aircraft model performing symmetric and antisymmetric maneuvers at Mach 0.85.