Morphology of silicon nanostructures obtained by thermal chemical vapour deposition (CVD) method in mesoporous silica particles (mSiO2) and macroporous synthetic opal were studied. The proposed method allows obtaining a uniform Si layer on the surface of non-porous spherical silica particles forming macropores in opal, in contrary, to complete filling of 3-nm pores inside mesoporous particles with amorphous silicon. The thermal CVD provides for gradual change of pore filling which, in turn, leads to step-to-step variation of porosity characteristics in the case of mSiO2/Si and the modification of photonic crystal properties in the case of opal-Si.