A comparative study of AFM and SEM imaging of the same area of a human scalp hair has been carried out to determine the similarity and the differences between the two techniques. Sample preparation for SEM analysis requires a metallization step and vacuum exposure, both of which could potentially induce modifications to the surface details. By contrast, AFM is a suitable technique to evaluate any effect resulting from sample manipulation because it can be applied without any specific treatment. AFM analysis demonstrates that sample metallization is responsible for modifications to the surface details of hair, mainly comprising an increase in height of scale steps and of root mean square roughness together with variation in scale profiles. Sample treatments for SEM imaging are in general potentially responsible for surface modifications to the samples involved.