Hi Sundip, I would not expect the roughness of a film to change the refractive index, as it is a bulk property of a material. Having a rough film however will make measuring the refractive index very challenging.
The real part of the RI should not change - unless the preparation conditions have altered the stoichiometry - but one would expect the imaginary/absorptive component to increase.
The refractive index (RI) of a material is in general a complex number, corresponding to the change in propagation speed of light through it owing to the dielectric interactions plus the losses caused by the ionic interactions.
As I understand, thickness affects both dielectric interactions and losses of the film. So refractive index should change with roughness.
You can check our paper where we have calculated the complex RI of graphene oxide in response to gas. Gas absorption by graphene oxide changes its thickness and accordingly the RI values change.