Surface roughness is one of the important parameters affecting the optical scattering loss of dielectric waveguides. Despite extensive research interests in correlating optical losses with surface roughness, not much research focus has been dedicated to the study of an accurate metrology and measurement standard for the characterization of waveguide roughness. In this Letter, we report an effective metrology for the measurement of waveguide surface roughness, using confocal laser scanning microscopy (CLSM). We also provide the definition of surface roughness relevant to CLSM terminology based on the measured peak-to-valley (P-V) values, which can be correlated to the conventional root-mean-square roughness, by employing multi-dimensional statistical models. Finally, we demonstrate the use of CLSM metrology in measuring two-dimensional roughness of 10 μm×6 μm silica waveguides, showing an average top surface roughness of 0.151 μm and an average sidewall roughness of 0.203 μm. For comparison, the scanning electron microscopy (SEM) measurements are also carried out for the same waveguide samples, and then the measured sidewall roughness values are in the range of 0.08-0.12 μm. Since SEM measures only the amplitude of roughness profile, while CLSM measures the P-V value, after doubling the SEM value, these two methods can provide comparable results of roughness.