In this study, clad layers of iron-based alloy with a nature of self-fluxing were melted on low carbon steel by plasma cladding process. Nanoindentation with atomic force microscopy (AFM) has been used to investigate the mechanical properties of the coating. Hardness and elastic modulus at ultra-low loads were first determined using the method proposed by Giannakopoulos and Suresh (G&S method). The true contact area and mechanical properties were then determined using atomic force microscopy (AFM) combined with the Oliver and Pharr method (new proposed method) as the correction group. The mechanical properties calculated by the two methods showed the same distribution while had deviation in specific values. The effect of surface roughness to the calculated mechanical properties was investigated. Both hardness and elastic modulus were found to exhibit certain surface roughness dependence. When root mean square (RMS) roughness ranged from 2.2 nm to 4.4 nm, hardness calculated by both the methods increased obviously and reached maximums around 4.1 nm. Elastic modulus calculated by G&S method at different RMS showed the same distribution with that of hardness, while reduced elastic modulus obtained by AFM was insensitive to the range of RMS. (C) 2010 Elsevier B.V. All rights reserved.