At present, indentation is considered as the most convenient approach for characterising materials for MEMS and even NEMS devices. Here, we demonstrate that a very slight change in the average surface roughness (Ra) of a commercial silicon wafer, that is, from 1.6 to 4.4 nm, can dramatically alter the indentation result. Another surface condition, namely, wetting, is also influential. Since it is not easy to quantitatively describe the effects of the interface between the indenter and tested material, the results of indentation test, as an approach for revealing the properties of a material, should be treated with great cautions.