Fast fourier transform (FFT) filtering has been used to remove unwanted frequencies (noise) in atomic force microscope (AFM) images of Cyclopore and Nuclepore membranes of nominal pore sizes 0.1 and 0.015 mu m, respectively. Such unwanted frequencies can result in initial production of distorted images, typically showing apparent pore elongation, especially with the use of cantilevers of low spring constant, higher scanning rates and for smell pores. The distorted images are associated with markedly asymmetric power spectra. Application of filtering to restore the symmetry of the power spectra results in images showing the true pore shape. This filtering technique is a powerful asset in AFM studies of membranes, especially those of small pore size.