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In order to apply secondary ion mass spectrometry (SIMS) to quantitative analysis of submicron areas, we made a high‐spatial resolution SIMS (submicron SIMS) by combining a focused metal ion beam, a plane‐focusing mass spectrometer, and a multichannel parallel detection system. A 35 kV, 100 pA beam with diameter on the sample of ≪0.1 μm was used. During measurements, this high‐current density ion beam can destroy the sample with a large sputtering rate when slowly rastered. This causes rapid changes in both absolute and relative intensities of secondary ions. In our system, a 120‐channel parallel detector covers the 1:2 mass range of m/e dispersion. By using this submicron SIMS, quantitative factors in the analysis of microstructures on the surface were investigated. Sputtering yield and, consequently, secondary ion intensity depend largely upon the angle between the primary beam and the sample surface just under the beam irradiation; such topographic effects distort the quantitative results. In order to avoid such distortions, it was found to be advantageous to shave off the analyzed feature from one edge to the other. By using such a sputtering method, the incident angle of the primary beam to the surface being sputtered is held constant. Accordingly, the quantitative power of submicron SIMS was greatly improved.