Abstract: An improved method of height measurement and correction for a two-stage deflection ("fly's eye" lens) electron beam accessed lithography system is provided which employs a height measuring transducer such as a capacitance gauge or an optical gauge and a two position fiducial calibration grid (LFG) set at positions LFG1 and LFG2 a known distance apart and wherein the electron beam of the electron beam lithography system is sequentially deflected to the two positions for each lenslet being corrected. Measurement signals derived at each position are processed pursuant to a unique algorithm to derive desired height correction output signals and height corrected deflection signals for control of the fine deflector of the electron beam lithography system.