Continuous-wave heterogeneous sonochemical method was developed to synthesize 3D assemblies composed by QDs of metastable (cubic) modification of CdSe with sphalerite structural type. 3D QD assemblies were deposited in thin film form and as bulk precipitates. Structure, surface morphology, optical absorption as well as charge carriers’ and phonon confinement effects were studied in details. The average nanocrystal radius, calculated by the Scherrer and Williamson–Hall methods, diminishes from 2.7 nm for samples synthesized by conventional colloidal chemical route to 2.0 nm for samples synthesized by sonochemical route. Upon post-deposition thermal annealing this value increases to 12.0 nm. QD size decrease is followed by increase of the uni-directional lattice strain and dislocation density (as defined by Hirsch), as well as by decrease of the lattice constant value. Previous findings were justified by analysis of X-ray diffraction peaks shape, which were found to be dominated by the particle size-distribution, instead of non-uniform strain. The energy of the fundamental direct \(\Gamma_{8}^{v} \to \Gamma_{6}^{c}\) interband electronic transition, computed from optical absorption data within parabolic approximation for the dispersion relation, shifts from 2.67 eV for sonochemically deposited samples and 2.08 eV for chemically deposited ones, to 1.77 eV upon post-deposition thermal treatment (close to the bulk value of 1.74 eV). The type of “interband” transitions does not change upon dimensionality reduce. Enhanced band gap energy blue shift upon average QD size decrease is followed by oscillator strength increase. Such trends were rationalized in terms of 3D confinement effects on charge carriers’ motion. Experimentally observed band gap energies agree very well with the predictions of the effective mass model of Brus. The next direct interband electronic transition, from the spin–orbit split component of the valence band to the conduction band, has been detected and analyzed. The 1LO bands in the Raman spectra of chemically and sonochemically deposited samples appear at 206 and 204 cm−1, as compared to the bulk value of 210 cm−1. The extent of homogeneous broadening of the corresponding band is larger in sonochemically deposited samples, indicating enhanced frequency of phonon–phonon collisions in smaller QDs. The observed frequency shifts are dominated by phonon-dispersion terms, instead of lattice contraction.