I have certain metallic films treated via ion beam irradiation. I am analyzing the evaluation in topographical features. I have used NANOSURF FLEX AFM for the particular characterization. For analysis, I am using the recommended software which comes with the system. We are provided with different options (filters & signals) to present our micrographs. When we change these options, the area roughness changes significantly. For example, choosing the default setting of line fit shows normal roughness, however, changing the filter to derived data also changes area roughness decreases. Similarly, when we change the signal type from the z-axis to amplitude or phase, the roughness also changes.
I have consulted the literature and found that different approaches are used in different studies. I will definitely report the filters and signals I will be using for analysis. My question is which option is most viable for absolute area roughness.