In order to generate the digital gear tooth surfaces (DGTS) with high efficiency and high precision, a method for identification and compensation of machining errors is demonstrated in this paper. Machining errors are analyzed directly from the real tooth surfaces. The topography data of the part are off-line measured in the post-process. A comparison is made between two models: CAD model of DGTS and virtual model of the physical measured surface. And a matching rule is given to determine these two surfaces in an appropriate fashion. The developed error estimation model creates a point-to-point map of the real surface to the theoretical surface in the normal direction. A "pre-calibration error compensation" strategy is presented. Through processing the results of the first trail cutting, the total compensation error is predicted and an imaginary digital tooth surface is reconstructed. The machining errors in the final manufactured surfaces are minimized by generating this imaginary surface. An example of machining 2-D DGTS verifies the developed method. The research is of important theoretical and practical value to manufacture the DGTS and other digital conjugate surfaces.