A neural prosthetic device can selectively deliver light to different cortical layers, at different depths, in the brain. The device includes LEDs and corresponding waveguides that can extend into the brain. At least two of the waveguides have different lengths. The neural prosthetic device or other devices can be manufactured by changing the hydrophilicity or lyophilicity of a portion of a substrate layer, then depositing uncured polymer on the treated portion of the substrate layer. The uncured polymer flows under the influence of surface tension to form a volume. The volume is shaped as a dome that extends laterally to a boundary between the treated and untreated portions. The polymer is cured in discrete regions through the substrate layer. The discrete regions extend longitudinally from the substrate layer to a curved surface of the dome. The uncured portion of the polymer is removed. The cured regions form the waveguides.