Hi Viresh,
That is the pigment of the retinal pigment epithelium. If you are examining larvae, you can use PTU (1-phenyl-2-thiourea) to prevent the melanin from developing and be able to see the retina that way. If you are doing histology on adult retinas, you will need to remore the retinal pigment epithelium to visualize the retina.
Jenny
Post-doctoral Fellow, Raymond Lab
University of Michigan