Precise microanalytical techniques are essential in many fields such as cultural heritage materials, showing complex layered microstructures containing a wide range of materials of diverse nature and hardness. Noninvasive sample manipulation and preparation is required to avoid, as much as possible, sample contamination, which may strongly limit the materials identification. The method proposed consists in the application of thin gold or carbon protecting layers before embedding the samples in synthetic resin for microtoming. The validity and optimal procedure is checked for those materials most often found on the surface of paintings: varnishes (natural resins and wax). An artwork sample is similarly prepared and analyzed by optical microscopy (OM), scanning electron microscopy (SEM/EDS), micro-infrared spectroscopy (µFTIR/µSR-FTIR), and X-ray diffraction (µSR-XRD) with synchrotron light.