This paper deals with the surface analysis of spherical polymeric optical micro-resonators in order to correlate surface defects with optical characteristics. Atomic force microscopy was used on structures to determine surface quality, which is the main origin of optical scattering losses. Surface morphologies were numerically treated to enable a relevant investigation on surface parameters such as root mean square (RMS) roughness (30.1 +/- 3.0 nm) or correlation length (few microns) necessary to express optical quality factors. A statistical analysis was conducted for calibration of these parameters as a function of cavities’ diameter. Results are in perfect agreement with spectral analyses performed in parallel on others structures. This comparison highlights the main role of scattering losses on quality factor origin.