Here is one of the nifty things you may use fft filtering for.
The laser scanning confocal microscope scans along the X axis. If there is noise in the laser, then this shows up most dramatically in adjacent X axis scans. Filtering the frequency of the alternating X axis intensities cleans up the image.
|The original image. Reflectance mode of the confocal using the 458 nm line of an Ar laser. Note the horizontal lines.||The power spectrum calculated by ImageJ 1.32h with contrast enhanced to show the bright spots that represent the X axis fluctuation.||The power spectrum with masks drawn on it.||The inverse transform applying the masks.|
The Image Processing Toolkit also does this in Photoshop.