Powerful femtosecond laser pulses that propagate through narrow ablating capillaries cause modification of capillary walls, which is studied experimentally and theoretically. At low intensities, laser-induced periodic surface structures (LIPSS) and porous coating composed of sub-micron particles appear on the walls. At higher intensities, the surface is covered by deposited droplets of the size up to 10 µm. In both cases, the ablated material forms a solid plug that completely blocks the capillary after several hundreds or thousands of pulses. The suggested theoretical model indicates that plug formation is a universal effect. It must take place in any narrow tube subject to ablation under the action of short laser pulses.