Abstract Scan projection lithography onto fine cylindrical specimen surfaces was investigated. The reticle was scanned in the direction perpendicular to the specimen axis, while the specimen was rotated. The momentary exposure area was limited by a narrow slit with 0.3–0.6 mm width. When the perpendicularity and the synchronization between the scan and the rotation stages were precisely adjusted and the waggles of the specimens were suppressed using the newly contrived specimen guide, patterns were printed with high accuracy on all the circumference surfaces of the specimens. The technology was applied to the fabrication of axial pump shafts by etching the helically patterned specimens. The shafts were assembled into actual pump systems. Adopting an idea of making the helicoids direction inverse at the driving end of the pump shaft, coloured water was successfully pumped out through a micro-tube with 300 μm inner diameter by a flow rate of 16–84 μl/min.