Yes, coherence scanning microscopes can measure "roughness" in the nm-range. However, this makes only sense for very smooth surfaces and one would better call this a "waviness" measurement, because all small structures are "filtered" due to the limited wavelenght of the light. And "seperating structures" that are in the range of the difraction limit (=structures become visible in the microscope image) is one thing, calculating a useful hight value from such data is another thing.
If "nano-sized" refers to lateral dimensions, the answer is clearly no.