An accurate control of the optical properties of single crystal diamond during microfabrication processes such as ion implantation plays a crucial role in the engineering of integrated photonic devices. In this work we present a systematic study of the variation of both real and imaginary parts of the refractive index of single crystal diamond, when damaged with 2 and 3 MeV protons at low-medium fluences (range: 10^15 - 10^17 cm^-2). After implanting in 125x125 um^2 areas with a scanning ion microbeam, the variation of optical pathlength of the implanted regions was measured with laser interferometric microscopy, while their optical transmission was studied using a spectrometric set-up with micrometric spatial resolution. On the basis of a model taking into account the strongly non-uniform damage profile in the bulk sample, the variation of the complex refractive index as a function of damage density was evaluated.
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