We have used atomic force microscopy (AFM) to measure the snap-off forces between a micron sized flat silicon AFM tip and a rough Si(0 0 1) surface. The current paper is a natural continuation of our previous paper (Çolak et al., 2014), dealing with snap-off forces between an identical flat tip and flat Si(0 0 1). Within the applied experimental parameter windows we observed no dependence of the snap-off forces on the applied normal loads (3–18 μN) and residence times (0.5–35 s) for the current flat-on-rough geometry as was the case for the former flat-on-flat geometry. The snap-off forces were found to increase with relative humidity in both geometries. As in the case of the flat-on-flat contact geometry, a strong dependence of the snap-off forces on the retraction speed of the tip was observed. Here, we find a strong decrease of the snap-off forces with increasing tip speed, especially at low velocities in the range 40–1000 nm/s for the flat-on-rough geometry. This is in contrast with the flat-on-flat geometry, where we found a strong increase of the snap-off force with increasing tip speed. These observations are explained in terms of a cross-over of the importance of capillary forces and viscous forces. We suggest that the relative importance of both forces can be checked via variation of the tip speed.