The microstructure and the local wettability of functionalized patterns is reported. The patterns are formed by the photolithographic structuring of multilayers of hairy rod polymers on glass/MgF2/SiO2 substrates. By application of quantitative reflection interference contrast microscopy (RICM), the RICM image analysis was improved by accounting for (i) multiple reflections and the finite illumination aperture in stratified systems and (ii) geometrical effects in wedge-shaped systems and by (iii) optimizing the contrast enhancement through adjustment of the MgF2 coating. The surface free energy of hairy rod films were determined by analysing the contact angle of partially wetting liquid droplets as a function of the surface tension of the liquid. Periodic lattices of hydrophobic domains separated by hydrophilic domains were applied to check the theory of Joanny and de Gennes [J. Phys. Chem. 81, 552-562 (1984)] of contact angle hysteresis at periodic arrays of pinning centers. Measurements of the shape of the triple line and the contact angle hysteresis by RICM confirmed the theoretical predictions.