In this article, it is demonstrated that atomic force microscopy (AFM) can be useful for observing surface microstructures on the bottom of contact holes used for large scale integrated devices. The AFM employs a zinc-oxide (ZnO) whisker tip with high-aspect ratio and a hopping scanning mode operation. In the hopping scanning mode operation, the probing tip is moved up and down with a period synchronized with the movement in the x direction to avoid collisions against the acute protrusions. Some kinds of bottom surfaces of the contact holes with a diameter of 1 mum and a depth of 1.5 mum have been successfully imaged with nanometer-scale resolution by this AFM technique.