The Electrical Discharge Machine(EDM) which can process metals of any hardness, is generally used for making moulds and dies. During the process, because the process is non-contact, unlike milling, drilling or grinding, a large machining force does not seem to exist. However, when using a large electrode, a large machining force is generated by the viscosity of the dielectric liquid. Such force deforms the machine and makes the machined depth several tens to hundreds of micrometers less than the required depth. As a result, additional machining for the shallow areas is required, which obviously increases total machining time.<br>To cope with this problem, we have proposed a new method to utilize a disturbance observer to compensate for the discrepancy in the depth, according to the estimated value of the deformation. The disturbance observer is designed based on a mechanical model identified by modal analysis, in which a machining force is considered as step disturbance. With the proposed method in an actual machining, although the value of deformation is up to about two hundreds micrometers, the error in the depth is kept within a few micrometers. It does not need any additional machining for realizing the required depth, and the total machining time is about 40% shorter than for the conventional method. This result confirms that the proposed method is essential for accurate and fast machining where a large machining force is present.