Embodiments described herein relate to methods for fabricating waveguide structures utilizing substrates. The waveguide structures are formed having input coupling regions, waveguide regions, and output coupling regions formed from substrates. The regions are formed by imprinting stamps into resists disposed on hard masks formed on surfaces of the substrates to form positive waveguide patterns. Portions of the positive waveguide patterns and the hard masks formed under the portions are removed. The substrates are masked and etched to form gratings in the input coupling regions and the output coupling regions. Residual portions of the positive waveguide patterns and the hard masks disposed under the residual portions are removed to form waveguide structures having input coupling regions, waveguide regions, and output coupling regions formed from substrates.