We have produced nanocrystalline titanium dioxide films with different structures (anatase or rutile) by depositing mass selected clusters from the gas phase. Nanoparticles are produced by a pulsed microplasma cluster source and are selected by aerodynamic separation effects. We have characterized nanocrystalline films by Raman spectromicroscopy and transmission electron microscopy, showing that the films assembled with very small clusters have a predominant rutile phase, whereas larger clusters form films with anatase structure. Our observations suggest that phonon confinement effects are responsible for a significant shift and broadening observed for the Raman peaks.