In this work, the nanoscale surface morphology of n-Si silicon single crystals with a (111) crystallographic orientation was investigated using atomic force microscopy. A comparative analysis was carried out for as-grown and neutron-transmutation-doped n-Si samples. The AFM images reveal that the as-grown n-Si (111) surface is characterized by a non-uniform nanoscale relief with local peaks, valleys, and island-like formations within a height range of approximately 0–12 nm. These morphological features may be related to growth-induced surface imperfections, oxygen-associated structural formations, and local microstructural inhomogeneities. After neutron-transmutation doping, the surface morphology becomes noticeably modified, showing a relatively more uniform and compact nanoscale relief. The obtained results indicate that neutron-transmutation doping affects not only the electrophysical properties of silicon single crystals but also their surface state and nanoscale topography. These findings are important for evaluating surface quality, defect distribution, and doping-induced structural changes in n-Si-based microelectronic and nanoelectronic devices.