Ionoluminescence (IL) produced by MeV/amu particles in the Nuclear Microprobe carries rich information on the nature of the chemistry and physics in the various types of materials, such as the molecular structure and ion's valence, etc. IL/PIXE methods offer unique ways to study the general luminescence phenomenon by directly relating the trace element information provided by PIXE to IL spectroscopic results. The IL can also be used to identify the organic molecular structure, hence, the combination of the IL data with the PIXE elemental data provide a new tool for biology and medicine studies. One example is the epidermis from the human skin, which exhibits a clear IL. IL is very sensitive to the local chemical environment conditions of the excitation point, therefore, it can be very effective to study the beam modification and beam damage effects. The beam damage problem in the Nuclear Microprobe applications is discussed.