The dopant distribution and surface and structural properties of Er- and Eu-doped GaN samples were investigated using atom probe tomography (APT) and atomic force microscopy (AFM). Erbium accumulation within host GaN threading dislocations was directly detected by APT allowing for the dislocations to be imaged in three dimensions. In addition, photoluminescence spectroscopy with high lateral resolution, by means of scanning near-field optical microscopy, was performed on Eu-doped GaN samples. By combining these results with AFM mappings of the same area, it was concluded that Eu3+ ions also accumulate at threading dislocations. Moreover, high-resolution surface profiles of both samples show that even dilute doping (<0.2%) of Eu and Er has a significant influence on the growth morphology of the GaN host material and the nature of the threading dislocations within it. Transmission electron microscopy techniques were used to show the influence of rare-earth incorporation on the growth of GaN lattice and the propagation of threading dislocations.