In image acquisition process, the quality of microscopic images will be degraded by electrical noise, quantizing noise, light illumination etc. Hence, image preprocessing is necessary and important to improve the quality. The background noise and pulse noise are two common types of noise existing in microscopic images. In this paper, a gradient-based anisotropic filtering algorithm was proposed, which can filter out the background noise while preserve object boundary effectively. The filtering performance was evaluated by comparing that with some other filtering algorithms.