This chapter presents a practical model-based decoupling control strategy tailored for multivariable mass–stiffness–damping systemsMass–stiffness–damping system (MKC systemsMKC system) exhibiting strong internal coupling and external disturbances. Systems such as multi-joint manipulators and rotor-bearing assemblies frequently suffer from cross-axis interactions that compromise control performance and stability. Traditional decoupling techniques often assume fixed linear dynamicsLinear dynamics and require complex transformations, limiting their practicality in real-world, time-varying applications. To address these challenges, the chapter introduces a linearModel-Following Control (MFC) model-following control (MFC)Enhanced Model-Following Control (enhanced MFC) scheme that achieves robust decoupling and disturbance rejectionDisturbance rejection using intuitive engineering constructs. By aligning plant behavior with a reference model through a simple compensator, the method attenuates dynamic couplingDynamic coupling and enhances stability—even under parameter variations or nonlinear perturbationsNonlinear perturbation. The approach is extended from frequency-domain to time-domain implementation using a state-space framework, making it well-suited for modern control systems. Comprehensive case studies on rotor-bearing systems validate the introduced method across different operating speeds, including open-loop unstable scenarios. Results demonstrate that the controller suppresses cross-coupled vibrations, tracks desired dynamics, and maintains performance with minimal redesign. Moreover, the framework scales naturally to multi-degree-of-freedom systems, providing a reliable, low-complexity solution for decoupling in complex mechanical systems. The adaptability of the method makes it ideal for integration with advanced techniques like adaptive and observer-based control in future extensions.