Photorefractive waveguides that are optically modifiable can be used as the adaptive interconnection channels for optical neural networks. We investigate experimentally a refined fabrication method for the photorefractive waveguides in a lithium niobate crystal. The experimental results show that nonuniform illumination by a discontinuous movement of the focus can fabricate a better optical waveguide than uniform illumination by a continuous one. The discontinuous movement of the focus reduces the spatial overlap between the successive exposures, and avoids the redistribution of the space-charge density formed previously. This refinement results in a narrower and clearer index distribution of the waveguide. We further show that good waveguides are fabricated if the focus is scanned in a particular scanning direction that makes a small angle with the plane perpendicular to the c axis of the crystal.