Modification of surface and volume of sapphire is shown to affect reflected and transmitted light at THz spectral range. Structural modifications were made using ultra-short 230 fs laser pulses at 1030 nm and 257.5 nm wavelengths forming surface ripples of ~250 nm and 60 nm period, respectively. Softening of the transverse optical phonon TO1 mode due to disorder was the most pronounced in reflection from laser ablated surface. It is shown that sub-surface periodic patterns of laser damage sites have also modified reflection spectrum due to coupling of THz radiation with phonons. Application potential of laser structuring and disordering for phononic engineering is discussed.