We investigated the effect of nanoscale fluctuations in the distribution of dopant atoms on the roughness of electronic interfaces of p-n junctions and on the formation of electronically separated dopant-induced dots. It is shown that the screening fields around each charged dopant atom and a clustering of dopant atoms induce two separate roughness components, which are much larger than the roughness of the underlying metallurgical interface. This leads to charge carrier depleted zones extending locally through the entire nominally homogeneously doped layer for layer thicknesses close to the cluster dimension. The results demonstrate that the clustering of dopants strongly limits the size of future devices by forming electronically separated dopant-induced dots, which introduce drastic changes in the current-voltage characteristics. (C) 2004 American Vacuum Society.