The aim of this study was to report the first discussion of statistical parameters and possible applications related to the surface of kefir biofilms prepared with Maytenus rigida Mart. extract through micromorphology, using atomic force microscopy (AFM). Four different samples were produced. The reference contained demerara sugar with a concentration of 40 g/L and the others had added extract whose concentrations were 0.25, 0.50, and 0.75 g/L, respectively. AFM was used to image the surface in tapping mode, on square areas of 30 μm × 30 μm. Images were studied by the MountainsMap premium commercial software. The main parameter of the surface, roughness, grew with the increase of the extract concentration up to 0.50 g/L. In addition, asymmetry and kurtosis showed that the biofilm with the best peak distribution was the one with 0.25 g/L of plant extract. The other parameters followed the main results for the surface and were observed for the depth and volume parameters. The power spectrum density spectrum confirmed the reliability of the results for the sample with 0.25 g/L. Therefore, the sample with 0.25 g/L of plant extract produced the best balance in relation to the surface properties. These results showed that the biofilm morphology and microtexture were affected by the incorporation of the plant extract and can be useful to define possible applications.