The regular periodontal practice of scaling and root planing produces a smear layer on the root surface that is detrimental to the readhesion of tissues during subsequent regeneration therapy. Although it has been demonstrated that gels containing the chelating agent ethylenediaminetetraacetic acid (EDTA) can assist in the removal of this contaminating layer, no quantitative method is yet available by which to evaluate the efficiency of the treatment. In this article, the power of atomic force microscopy (AFM) as a technique for monitoring and mapping the surfaces of dentinal roots is demonstrated. Roughness parameters of teeth that had been scaled and root planed were determined from AFM images acquired both before and after treatment with EDTA. The results confirmed that EDTA is an efficient cleaning agent and that dentinal samples free from a smear layer are significantly rougher than the same samples covered by a contaminating layer. AFM analysis is superior to alternative methods involving scanning electron microscopy because the same sample section can be analyzed many times, thus permitting it to be used as both the control and the treatment surface.