This article presents the results of experimental studies on the formation of nanosized objects in single crystals of silicon ion-implanted with manganese ions with an energy of 40 keV at various doses. The formation of nanosized objects was determined by atomic force microscopy (AFM) and Raman spectroscopy (RS). It was found that in the Raman spectrum of non-implanted samples there are peaks with a wave number of 520 cm-1 characteristic of pure silicon associated with the crystalline phase and satellites with frequencies 301 cm-1, and 971 cm-1. The band with a wave number of 971 cm-1 corresponds to the main band of the tetrahedral bond in silicon. The intensity of this peak depends on the sample thickness. When the sample thickness changes from 200 μm to 3 mm, the intensity of this peak decreases by almost two times. And in the Raman spectra of ion-implanted samples, several bands with different intensities are observed, and their number and intensity strongly depend on the implantation dose. It has been suggested that the observed peaks are possibly associated with radiation defects and nanosized formations. This assumption was verified using AFM investigation. The AFM images show various nanosized objects, apparently associated with manganese ions.