Separated nanocolumns (NCs) with embedded Si nanoclusters were prepared using the top-down technique that combines a bio-template and the defect-free neutral beam etching of Si0.75Ge0.25/Si/Si0.75Ge0.25 double-quantum-well layers. The electron spin resonance (ESR) was studied in the dark and under illumination for the structures with different lateral sizes of NCs. For the structure with a NC diameter in the range of 20-25 nm, the ESR signal is characterized by the isotropic line width. The spatial separation of nanoclusters results in the suppression of the Dyakonov-Perel mechanism of spin relaxation. A decrease in the NC diameter down to 13-14 nm leads to electron localization under the bottom of NCs, making the orientation dependence of the ESR line width anisotropic. Illumination results in the increase in spin lifetimes in both the types of NC structures, relocating the electrons to the center of NCs in the narrow NC structure, and making electron localization stronger in the thick NCs.