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Noise is a fundamental metrological characteristic of the instrument in surface topography measurement. Therefore, measurement noise should be thoroughly studied in practical measurement to understand instrument performance and optimize measurement strategy. This paper investigates the measurement noise at different measurement settings using structured illumination microscopy. The investigation shows that the measurement noise may scatter significantly among different measurement settings. Eliminating sample tilt, selecting low vertical scanning interval and high exposure time is helpful to reduce the measurement noise. In order to estimate the influence of noise on the measurement, an approach based on metrological characteristics is proposed. The paper provides a practical guide to understanding measurement noise in a wide range of applications.