This paper presents a sliding mode disturbance observer-based motion tracking control methodology. In particular, the methodology is applied to control a semi-automated hand-held ear surgical device for the treatment of otitis media with effusion. The proposed control methodology is utilised to deal with the undesirable effects in the motion system, such as non-linear dynamics, parametric uncertainties and external disturbances. It employs a proportional-derivative control scheme together with a sliding mode disturbance observer for rejecting the undesirable effects. The stability of the proposed control methodology is proven theoretically and its effectiveness is evaluated experimentally. In addition, promising motion tracking experimental results are shown, and it can be observed that the proposed approach offers more robust performance for controlling the hand-held surgical device and other similar instruments.