The plasma induced surface modification of Poly(methacrylic acid)-Poly(methylmethacrylate) copolymer (PMAA-co-PMMA) thin films has been characterized in this work by using a conventional Atomic Force Microscope (AFM). The polymer films, spin casted from methanol solutions, were exposed to different plasma discharges characterized by identical power supply and exposure but with different gas composition (Ar-N 2 mixtures). The effect of the treatments on the topographic and structural properties of the surfaces has been studied with the AFM acquiring the amplitude and the phase of the oscillating cantilever. The application of statistical tools to topographic images led to the determination of organization patterns in the copolymer films. These are of special interest in the case of Ar plasma treated samples since organized motives present dimensions below 50 nm. Regarding the materials properties, a phase contrast between the two polymers constituting the film, PMAA and PMMA, was detected. Both, the evolution of compositional intermixing and the dimensions of organized motives could be ascribed to plasma energetic and chemical factors as determined from plasma diagnostic techniques. These results confirm that plasma processes are key tools towards the controlled surface modification of copolymer films.