Abstract Non-raster scanning can increase the scanning frame rate and measurement speed of atomic force microscopes (AFMs). It is also possible to correct the 3D drift during the non-raster scanning. However, the algorithm for the drift correction depends upon the properties of each scan pattern. While localised non-raster scanning using a rosette scan may be faster than the frequently used Lissajous scanning patterns, the drift correction is more challenging because the scan has crossing points only in local neighbouring segments where there are short temporal and spatial separations of the crossing paths. This design note presents a novel solution that successfully overcomes this problem and extends a drift correction method previously developed for Lissajous scans to the 3D drift correction of localised non-raster scanning using a rosette scan trajectory. The drift in the X, Y and Z axes can be determined using the crossing points and locally repeated scans of the same features. The general procedure is presented together with experiments using rosette scans of a two-dimensional lateral calibration standard. Experimental results have demonstrated that the method can effectively correct both the drift in the three axes and sample tilt, leading to significantly improved images. The method requires only localised crossing points in the scan and does not need additional scans to determine the three-dimensional drift based on cross-correlation and least squares techniques, and it can be used with any AFMs capable of rosette scanning.