FIB-SEM images are often accompanied by stripe artifacts created due to inhomogeneous milling. The removal of these artifacts plays an essential role in ensuring proper post-processing such as data analysis or segmentation. We present a robust variational method to remove stripe artifacts effectively in 2D and 3D images and demonstrate its capabilities on several examples. The tool is widely applicable to improve quality as well as facilitate downstream processing and analysis of images acquired on systems that do not provide hardware-based destriping methods. The method was successfully applied to FIB-SEM, light sheet (fluorescence) microscopy and remote sensing images.