In the indentation test, the hardness and the elastic modulus depend strongly on the estimate of the indenter-material contact area at peak load. However, many elastic–plastic behaviours such as elastic recoveries during unloading and piling-up or sinking-in of surface profiles during indentation affect the determination of the hardness and the elastic modulus. So, atomic force microscopy is a method of utmost importance to provide an accurate knowledge of the indentation impression especially when plastic deformations occur, that leads to errors in the determination of the contact area. Atomic force measurements of vanadium, tungsten, molybdenum and tantalum pure metals as well as stainless steels, often used as substrates for thin films depositions, highlight the difficulties to estimate the contact area. The variation of hardness values determined by atomic force microscopy measurements and nanoindentation test is correlated to the formation of folds of 150 and 100 nm high, around the residual impression of vanadium and tungsten indented at 0.1 N, respectively. Some folds which increase with increasing loads are detected on the residual impressions of both 35CD4 and 30NCD16 stainless steels indented under loads of 0.01 N, only. Such structures are related to pilingup of surface profiles that could lead to an underestimate of the contact area in the indentation test. So, the hardness value of tungsten could be closer to 6 than to 7 GPa whereas the effect of piling-up on the estimation of contact area of vanadium could be lower. Almost no deformation is seen on tantalum and molybdenum. So, the hardness values determined by the various methods are consistent. These results show that atomic force microscopy measurements are quite complementary of the nanoindentation test.