What do you mean by "macroscopic roughness"? The roughness Gwyddion determines is the roughness that is found on the scanned area, it does not care whether it is small or large.

Hello Yazan,

What do you mean by "macroscopic roughness"? Usually you can obtain different roughness values ​​from AFM images with different scales (Such as 1x1 um and 10x10 um). For the same sample, you could obtain different RMS, however this not means "macroscopic roughness", it is just roughness.

The values ​​presented by Gwyddion need to be interpreted properly, since it provides several values for roughness. An important point is to measure the roughness in several parts and perform some statistical analysis.

Dear Yazan,

according to the answer before mine, the key is the balance between the homogeneity of your sample and your scanned area. "Macroscopic" term should be misleading and roughenss should be related to the investigated area. However if your Macroscopic means the measure obtained with a roughness tester then your result should be considered representative as "macroscopic roughenss" if there is no correlation between the values coming from subsequent points so that you are observing an area larger than typical surface topography variations. By the operative point of view you can make two checks: first, move with your cantilever in different zones of your sample and If you will find similar results as a rule of thumb this figure should be considered as representative for macroscopic in your system. Second one, try to increase progressively your scanned area by using AFM or even by changing technique. Again, if for example the results coming from 10x10 microns are close to the one 1x1 mm then you can consider this as representative for macroscopic.