Abstract Because interfaces have important implication for processing and device performances, atomic force microscopy (AFM) has been used to investigate both the (100) Si surface morphology and the topography of the buried oxide-silicon overlayer interface of low-dose separation by implanted oxygen (SIMOX) materials. The mean roughness measured on the silicon overlayer surface is about 0.5 nm, and is flattened by a factor two when using additionnal annealing steps. A square-mosaic rugged morphology has been observed on the buried oxide-silicon overlayer interface of samples annealed at 1320 °C for 6 h under an Ar-O 2 atmosphere. This morphology has been related to the interface regrowth of the implantation-damaged silicon. These square structures have a root-mean-square (r.m.s.) height of 1–3 nm, and are flattened during additional annealing steps at 1320 °C under Ar-O 2 . Nanometer scale investigations by AFM have been used to analyse the microstructural changes found on the silicon-on-insulator (SOI) layer after additional annealing steps.