X-ray steppers have been developed and improved to the point where they are capable of replicating 100-nm patterns. The alignment system, which employs an optical heterodyne system with two wavelengths, was improved by analyzing and reducing the crosstalk and asymmetry in the alignment optics. The overlay accuracy of the steppers with respect to themselves is better than 20 nm, regardless of the wafer mark depth. A magnification correction method using wafer temperature control and chucking force is implemented on the steppers. We have achieved an overall overlay accuracy of less than 35 nm, which includes the pattern placement error for two masks, etching process distortion, and alignment error. This demonstrates the capability of proximity X-ray lithography to meet the requirements of 100-nm lithography.