We have developed a two-step microextrusion technique to align lipid nanotubes of 200 nm in diameter in parallel on planar glass substrates. This technique is useful to align self-assembled molecular nanofibers or nanotubes with diameters ranging from 100 to 300 nm. In the first step, we applied relatively large air pressure (approximately 40 hPa) onto a microcapillary filled with aqueous dispersion of lipid nanotubes to push them out. An aqueous droplet with 60 microm diameter was then extruded from the tip of the microcapillary. After one end of the lipid nanotube moved out, we changed the air pressure to be smaller, approximately 20 hPa to reduce the flow rate of the dispersion. The decrease in size of the droplet allowed us to fix the exposed end of the lipid nanotube onto the planar substrate. By dragging the microcapillary along the planar surface, we were able to align the whole nanotube onto the substrate. Using this technique, we have achieved the parallel alignment of the lipid nanotubes on the glass substrate.