SrTiO(3)(100) single crystals with high donor dopant concentrations (5 at% La) were annealed at 1000 degrees C for up to 150 h in ultrahigh vacuum (UHV). By applying scanning tunneling microscopy (STM) nanostructures are observed on top of the surface with typical diameters of 20 nm and typical heights of 8 nm. To characterize their electronic structure and chemical composition, the surface was analyzed by metastable impact electron spectroscopy (MIES), ultraviolet photoelectron spectroscopy (UPS), scanning tunneling spectroscopy (STS), and depth profiling Auger electron spectroscopy (AES). Investigations of the stoichiometry suggest that the secondary phases consist of LaTiO(3). We present a defect chemistry model which attempts to explain the observed effects.