Restoration and conservation procedures for historical musical instruments involve several issues, also connected with their frequent being played. One of the most delicate procedures for their preservation is the cleaning of surfaces from soil and dirt which have accumulated over the years. In fact, when external particles reach the surface, a fraction of them can deposit on it. Moreover, the contact with the player can generate chemical-physical changes, rapidly warming and wetting the surfaces through sweat deposition. This work focused on the cleaning methods of surfaces of bowed string musical instruments by a systematic and analytical approach. The selective cleaning procedure of varnished surfaces from grime and soil needs to be performed without compromising the original matter. Therefore, a dirty surface was reproduced on a set of varnished mock-ups and different water-based cleaning systems—generally used by restorers—were tested. The procedures were monitored in each step with several analytical methods: multispectral imaging (near-infrared (NIR), IRFC, visible imaging (VIS), UV-induced visible fluorescence), stereomicroscopy, XRF and FTIR spectroscopies allowed us to non-invasively outline the cleaning system efficacy. The results highlighted different levels of cleaning and, in some cases, it was possible to identify the best selectivity for the different procedures.