<p dir="ltr">This research focuses on the advanced motion control of mechatronic systems that exhibit flexible modes and contain nonlinear disturbances, such as Coulomb friction and gear backlash. Two types of flexible mechatronic systems: (1) cable-pulley actuated lifting systems and (2) large servo-table systems with small inertia on the motor side and large inertia on the table side, are comprehensively studied with detailed system modeling and analysis.</p><p dir="ltr">In particular, in-depth system identifications of the large servo-table have been conducted, revealing the complex high-frequency flexible modes. Fitting models via MATLAB are obtained based on the frequency responses in experiments, which are further used as the nominal model to reveal the effect of the flexible modes on the closed-loop system stability. A novel nonlinear two-mass model that accurately captures the system dynamics, including flexibility in the table's shaft, Coulomb friction in the bearing, and gear backlash, is built and successfully validated in experiments.</p><p dir="ltr">A broad range of control strategies, from traditional linear time-invariant (LTI) designs to the more advanced simplified direct adaptive robust controls (S-DARC), are evaluated and validated through simulations and comparative experiments on the large servo-table system. These results demonstrate the superiority of the ARC approaches for robust motion control of mechatronic systems with flexible modes and nonlinear disturbances. </p><p dir="ltr">For the first time, novel nonlinear indirect adaptive robust control designs are introduced to enhance system robustness and tracking performance in the presence of complex high-frequency flexible modes. These include the $H_{\infty}/\mu$-based nonlinear indirect adaptive robust control ($H_{\infty}/\mu$-based IARC) and a nonlinear indirect adaptive robust control approach to disturbance observer design (DOB-type IARC). Comprehensive simulations and experiments are conducted to validate the effectiveness of the proposed strategies. In addition, these two approaches are further extended to a generalized formulation of the $H_{\infty}/\mu$-based IARC, combining the strengths of both approaches.</p>