To improve the surface accuracy of the optical elements, the ion beam removal function was accurately fitted. Taking the root mean square (RMS) value of the removal function as the analysis object, the removal and fluctuation amount of the ion beam equivalent removal under different stacking spacings were analyzed. The feasibility of one-dimensional equivalent removal was verified on ground of theoretical and experimental data analysis, and the optimal stacking spacing was σ. With σ as the stacking spacing, the theoretical and experimental analyses of two-dimensional equivalent removal were carried out. Fused silica was used for 30 s two-dimensional equivalent removal experiments, and the removal value was 384.7 nm. The surface modification of fused silica plane window glass with the RMS of 138.5 nm (Φ100 mm) was carried out in combination with polishing experiment. The RMS was 18 nm after processing and the surface convergence rate reached 7.82.