Proper diagnostics of intense free-electron laser (FEL) X-ray pulses is indisputably important for experimental data analysis as well as for the protection of beamline optical elements. New challenges for beam diagnostic methods are introduced by modern FEL facilities capable of delivering powerful pulses at megahertz (MHz) repetition rates. In this paper, we report the first characterization of a defocused MHz 13.5-nm beam generated by the free-electron laser in Hamburg (FLASH) using the method of multi-pulse desorption imprints in poly(methyl methacrylate)(PMMA). The beam fluence profile is reconstructed in a novel and highly accurate way that takes into account the nonlinear response of material removal to total dose delivered by multiple pulses. The algorithm is applied to experimental data of single-shot ablation imprints and multi-shot desorption imprints at both low (10 Hz) and high (1 MHz) repetition rates. Reconstructed response functions show a great agreement with the theoretical desorption response function model.