The purpose of the present study was to investigate the surface topography of healthy enamel and dentine before and after application of a new chemomechanical system for caries removal, Carisolv. The same surfaces were investigated with respect to the influence of phosphoric acid, plus carious dentine after removal with either Carisolv or burrs. One-hundred freshly extracted teeth were used. Surface topography was measured in two different ways in order to characterize the surfaces at different levels of resolution, atomic force microscopy (AFM) and a contact stylus profilometer. Somewhat conflicting data were obtained with the two measuring techniques. When surfaces were investigated over a small area (AFM), healthy enamel seemed unaffected by Carisolv, while healthy dentine became smoother. Etching enamel with phosphoric acid resulted in a rougher surface, while no effect was detected on etched healthy dentine. Caries removal using Carisolv resulted in a smoother surface compared with conventional caries removal. When the surfaces were monitored with the contact profilometer, no effect of Carisolv could be detected on healthy enamel or dentine. Phosphoric acid etching, in contrast, increased the surface roughness of both enamel and dentine. When compared with conventional caries removal technique, caries removal with Carisolv did increase the surface roughness.