Atomic force microscopes (AFM) form images by sliding a sharp tip over a surface in a raster pattern and recording the height of the tip at each position. There is distortion in these images caused by a non-ideal shape and the size of the probe tips. Previously reported convolution and deconvolution algorithms have been implemented to study and simulate the interaction between the tip and the sample. The first part of this work is a comparison between AFM and Rutherford backscattering spectrometry (RES) data taken on nanometre size zinc islands on a flat substrate. Zinc islands were deposited on a silicon substrate using the ionized cluster beam deposition technique. An algorithm was developed to calculate the volume of the islands and the number of zinc atoms present from AFM images. The number of zinc atoms per unit area of the same samples was also measured by RES. The AEM and RES results agree qualitatively but there is an offset with AFM reporting more zinc than RES. A possible explanation for this difference is a convolution of the tip and sample making the islands appear larger. After deconvolution of the AFM images there was better agreement between AFM and RES on the number of zinc atoms per unit area.