The purpose of this article is to illustrate the use of two-dimensional fast Fourier transform (2D-FFT) algorithm to describe the properties of aluminium thin films. To do so, the microstructures of thin Al films deposited on stainless steel substrates though radio-frequency (RF) magnetron sputtering are analysed using two-dimensional fast Fourier transform (2D-FFT) algorithm. Field emission scanning electron microscope (FESEM) and atomic force microscope (AFM) images obtained on the surfaces of the films are taken through different image analysis processes. The power spectra are described in terms of spatial frequencies, wavelengths and light intensities in the reciprocal space for both SEM and AFM images. The results of power spectra obtained from FESEM and AFM micrographs are compared for two different cases-films deposited at 200 and 300 W at the same substrate temperature (100 °C). We observe that the 2D-FFT analysis of both SEM and AFM methods can describe (in more details) the distribution of surface structures in thin aluminium films.