All atomic force microscope (AFM) images suffer from distortions, which are principally produced by the interaction between the measured sample and the AFM tip. If the three-dimensional shape of the tip is known, the distorted image can be processed and the original surface form `restored', typically by deconvolution approaches. This restored image gives a better representation of the real 3D surface of the measured sample than the original distorted image. In this paper, we propose a method for estimating the three-dimensional shape of the AFM tip by measuring a micro-cylinder with a-priori known dimensions. The estimated tip shape is then used to restore subsequent AFM images, when measured with the same tip, under similar measurement conditions. Significantly, the impulse response of the AFM can be deduced using this method. The suitability of this novel approach for restoring AFM images has been confirmed using both computer simulation and also with real experimental AFM images. The proposed method is compared with standard restoration techniques and is shown to provide superior performance to such approaches.