The molecular properties and surface morphology of undoped and N-doped ultra-nanocrystalline diamond (UNCD) films deposited by microwave plasma CVD with addition of nitrogen are investigated with various spectroscopic techniques. The results of spatially resolved Raman scattering, ATR/FT-IR and XPS spectra show more amorphous and sp2/sp3 ratio characteristics in N-doped UNCD films. The surface morphology in AFM scans shows larger nanocrystalline diamond clusters in N-doped UNCD films. Incorporation of nitrogen into UNCD films has promoted an increase of amorphous sp2-bonded carbons in the grain boundaries and the size of nanocrystalline diamond grains that are well correlated to the reported enhancement of conductivity and structural changes of UNCD films.