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In the present study, the influence of water ageing on the surface characteristics of epoxy nanocomposites was analyzed through atomic force microscopy (AFM) studies. The hydrophobic properties of the epoxy nanocomposite material were analyzed through contact angle and diffusion coefficient measurements. Fractal dimension were calculated by adopting a multi resolution signal decomposition (MRSD) to the 1D-AFM signal through power spectral density calculations at each level of decomposition. 2D-MRSD studies were applied to AFM pictures to understand the surface characteristics of the material. The result of the study shows the presence of high and low frequency signals indicating characteristic variation in surface roughness of the material. The surface roughness parameter measured through the MRSD technique indicates that the surface roughness is lower for epoxy nanocomposites (upto 5Wt%) compared to pure epoxy resin. It is observed that the fractal dimension and the root mean square roughness values vary proportionately. Also it is realized that diffusion coefficient and surface roughness of the material shows an inverse relationship.