This study focused on identifying the effect of the laser wavelengths used in cleaning some manifestation damage appearing in pigments used on archaeological cartonnage preserved in the Egyptian Museum, Egypt. The manifestations of damage appear as mud, resin, color, dust and microbiological damage stains. Lasers were chosen as one of the modern applications that give good results when cleaning the pigment materials without making direct contact with the material. Accordingly, lasers with a wavelength of 532 and 1064 nm were tested to identify their effect on stains caused by pigments and to choose the best one for use in cases similar to those materials in the future. This study was conducted to identify the effect of the selected wavelengths and choose the best ones to apply to the archaeological model. The evaluations were conducted using several tests and analyses, such as digital microscopy, X-ray florescence, Fourier transform infrared spectroscopy, and Handy colorimetry to evaluate that effect of lasers with a wavelength of 532 and 1064 nm to remove stains. The experimental study demonstrated the good effect of the Nd:YAG laser with a wavelength of 1064 nm compared with that of the 532 nm laser. The results of using the Nd:YAG laser proved the good effect of removing all stains compared with the 532 nm laser, which caused big changes when used to clean the stains on the pigment’s surfaces; it also did not help in removing or reducing some stains such as mud stains. According to these results, the good effect of the Nd:YAG laser (1064 nm) make it more suitable for cleaning than that of the Nd:YAG laser (532 nm), which is not recommended for use as it gave bad results when applied.