The deposition of nanoporous carbon thin films with well-controlled morphology, high surface area and porosity is of great interest for different applications requiring autonomous and portable electrochemical devices for energy conversion and storage. The engineering of this class of devices and the evaluation of their performances require the measurement of the porosity and surface area of the active carbon layers. The quantitative characterization of these parameters by gas adsorption techniques is hampered by the small amount of material usually available on a thin film. Here we report a method based on the use of atomic force microscopy (AFM) and nitrogen adsorption technique for the quantitative characterization of the specific surface area and porosity of nanoporous carbon films. In particular, we apply it to nanostructured carbon films fabricated by supersonic cluster beam deposition (SCBD), studying the evolution of their structural properties with film thickness. We exploited the characteristics of SCBD in terms of high-throughput, stability, and reproducibility to fabricate films with controlled nano and microstructure over large substrates compatible with the requirements of gas adsorption measurements. Our approach demonstrates that the combination of AFM and nitrogen adsorption technique provides the possibility of undertaking systematic quantitative characterization of the nano- and mesostructure of cluster-assembled carbon films and of their evolution, which can be easily applied to porous thin films fabricated by many different techniques.