Atomic Force Microscopy (AFM) is no longer used as a nanotechnology tool responsible for topography imaging. However, it is widely used in different fields to measure various types of material properties, such as mechanical, electrical, magnetic, or chemical properties. One of the recently developed characterization techniques is known as loss tangent. In loss tangent AFM, the AFM cantilever is excited, similar to amplitude modulation AFM (also known as tapping mode); however, the observable aspects are used to extract dissipative and conservative energies per cycle of oscillation. The ratio of dissipation to stored energy is defined as tanδ. This value can provide useful information about the sample under study, such as how viscoelastic or elastic the material is. One of the main advantages of the technique is the fact that it can be carried out by any AFM equipped with basic dynamic AFM characterization. However, this technique lacks some important experimental guidelines. Although there have been many studies in the past years on the effect of oscillation amplitude, tip radius, or environmental factors during the loss tangent measurements, there is still a need to investigate the effect of excitation frequency during measurements. In this paper, we studied four different sets of samples, performing loss tangent measurements with both first and second eigenmode frequencies. It is found that performing these measurements with higher eigenmode is advantageous, minimizing the tip penetration through the surface and therefore minimizing the error in loss tangent measurements due to humidity or artificial dissipations that are not dependent on the actual sample surface.