If the height measurement you get is important (it nearly always is!), then yes, you should calibrate. Since the calibration is scale-dependent, when you want to make a very specific measurement, the best thing is to calibrate with a height standard that has a step of height close to the value you are interested in. So, in the case of atomic steps, you ideally want a sub- nanometre step. A suitable sample would typically be other monoatomic steps. On the other hand, if you are measuring things in the range of 100's of nanometers, a silicon grid with similarly sized steps is more suitable.