A method is proposed to extract pure Raman spectrum of epitaxial graphene on SiC by using a Non-negative Matrix Factorization. It overcomes problems of negative spectral intensity and poorly resolved spectra resulting from a simple subtraction of a SiC background from the experimental data. We also show that the method is similar to deconvolution, for spectra composed of multiple sub- micrometer areas, with the advantage that no prior information on the impulse response functions is needed. We have used this property to characterize the Raman laser beam. The method capability in efficient data smoothing is also demonstrated