Scanning Probe Microscopes (SPM) in general, and the Atomic Force Microscopy (AFM) in particular, have provided the unique possibility of 3D investigation of surface topography and access to material properties on the nanometer scale. Unfortunately, the surface is not perfectly probed by the AFM tip, due to its finite size. This fact leads to imperfections in AFM images and thus to errors in the roughness determination. These errors are particularly important when imaging highly corrugated surfaces. In this work we review this effects and another limitations of the roughness determination by AFM which in most cases are not taken into account. It is the hope of the authors that this mini-review serves to summarize our current understanding on problems associated to surface roughness determination by AFM, specially for those which are not familiar with this recent technique.