A method of fabricating a microstructure for an optical waveguide such as a photonic bandgap fiber is provided. The method includes the steps of assembling a stack of capillary tubes having substantially identical dimensions, fusing and redrawing the stack into a preform having a plurality of parallel holes of equal diameter, selecting a pattern of the holes for etching in order to increase their diameter, and plugging the unselected holes at one end of the preform against the flow of a pressurized etching fluid. Such plugging of the unselected holes is accomplished applying a layer of a gel-like sealant over the end of the preform, and then pushing the sealant into the holes to form sealant plugs in all of the holes. The sealant plugs are then removed from the selected holes by punching the sealant plugs out of the selected holes. The selected holes are then etched by conducting a pressurized flow of etching fluid to the end of the preform such that etching fluid flows only through the pattern of selected holes. The resulting preform is then fused and drawn into an optical waveguide, where the pattern of etched and unetched holes may form, for example, the microstructure for a photonic bandgap optical fiber.