This work establishes a multiscale and multitechnique nondestructive approach as valid methodology for monitoring surface properties and evaluating the effectiveness of enzymatic removal of varnishes from paintings/polychrome artefacts. Mock-up samples (documented reconstructions of oil, tempera, and gilded layers on canvas and wooden supports) were covered with different proteinaceous varnishes (egg white, animal and fish glue, casein) and then characterized before and after the removal of these coatings with enzyme-based solutions. The varnish was cleaned in several steps (two dry swabs and two wet swabs) with a clearance step for removing the residues from proteinaceous varnish or from enzyme solution. Microscopy [stereomicroscopy (SM), optical microscopy (OM), atomic force microscopy (AFM), and scanning electron microscopy (SEM)] and colorimetric (CIE L*a*b* system) techniques were used for characterization of the reconstruction surfaces at different scales (macro-scale by SM and OM; micro-scale by SEM and nano-scale by AFM). These techniques were also used to monitor the cleaning treatment. Although results presented in this work were obtained for the specific treatment of enzyme removal, the methodology could be extended to other types of materials and cleaning. Further experiments on real works of art are needed for a complete validation of the methodology.