This paper presents a systematic approach towards the control-oriented linear fractional transformation (LFT) modelling for the H∞ controller design of a non-linear multi-input multi-output (MIMO) system. A very interesting mechatronic platform, namely, twin-rotor laboratory scale helicopter, which is a highly non-linear and cross coupled dynamic system and pose challenges for many classical linear control techniques, has been considered as a candidate system to illustrate the proposed LFT modelling and the design of H∞ controller for non-linear MIMO system. A novel methodology has been presented to consider the model uncertainties arising due to the difference between the linearised mathematical model and the actual system, presence of disturbance signal, and the model order reduction during the derivation of the LFT model. A two-degrees-of-freedom (2-DOF) framework has been adopted for the design of the H∞ controller. Robust stability and performance of the resulting controller have been verified in simulation studies.