We propose a hybrid and flexible interference microscope combined with different phase algorithms to measure the surface roughness of thin films. Two phase measurement algorithms of the fast Fourier transform method and the five-step phase-shifting interferometry are used to evaluate the surface contour of aluminum-doped zinc oxide thin films coated using varying radio-frequency sputtering powers. The experimental results show that the proposed approach is feasible in determining the 3D deformation and surface roughness of thin films.