A registration method using the two‐stage standard mark system is developed for high accuracy overlaying of patterns on a deformed wafer in an electron beam lithographic system used for direct wafer writing of 0.5 μm very large‐scale integrated (VLSI) patterns. Deflection distortions are corrected according to heightzof a pattern writing field on a wafer. In this paper, deflection distortion correction and overlay accuracies are examined experimentally. Main field (2.6×2.6 mm) distortions are corrected using the third‐order power function of the main field coordinates (X,Y). Correction coefficients related to shift, deflection gain, and deflection rotation are shown to be a linear function ofz, in spite of varying the beam focusing level withz. Each distortion expressed in terms up to the third‐order power of (X,Y) can be corrected with an accuracy within 0.02 μm. Overlay accuracies within 0.12 μm (3σ) are yielded when two‐layer test patterns are exposed on a wafer deformed about 75 μm in theZdirection.