Femtosecond laser irradiation followed by chemical etching (FLICE) is a powerful and enabling technology for microstructuring glass substrates in 3D. The irradiated focal volume expresses increased etching selectivity with respect to the pristine material, enabling the fabrication of optical components with micrometric resolution, but with critical residual roughness (about 400 nm rms). Here we compare the surface quality of microlenses processed with different methods as CO2 laser annealing, thermal annealing in oven and polishing by direct dielectric barrier discharge inert gas plasma at atmospheric pressure. The optimized optical elements will be integrated on more complex devices for optical investigations of biological specimens.