The present invention relates to a method and a system for compensating interference in a charged particle beam microscopy system. A step of capturing data obtained from irradiation of a sample for a sampling duration can be implemented. In the system a respective data storage is provided for capturing and/or storing this data. Further steps of dividing at least representative parts of the sampling duration into time-windows and constructing, for each of the time-windows, an intermediate image, can be implemented. Detecting shift between the intermediate images and determining a compensation function for the shift between the intermediate images is realized as well. In a system the latter steps are automated by a respective processing component. The shift between intermediate images can be a two-dimensional shift and the compensation function represents a shift of the intermediate images in the two dimensions over time.