We prepared short microfibers comprising a mixture of a poly(methyl methacrylate)-poly(glycidyl methacrylate) copolymer and poly(methyl methacrylate) by electrospinning followed by ultrasonication treatment. The resulting short microfibers were 1.5 mu m in diameter and 5-30 mu m long. We then carried out surface-selective functionalization of the short microfibers using fluorescently labeled proteins. Microscopic observation revealed the lateral surface-selective and cross-section-selective modification of the short microfibers. Finally, we succeeded in the self-organization of the surface-functionalized short microfibers with polymeric microspheres to form complicated microstructures via specific interactions between biomolecules.