We describe here a preparation of pincushion structures with holes, hexagonally arranged microrings, and microdots by simple heating and peeling of self-organized honeycomb-patterned films. We have reported that the honeycomb-patterned films can be prepared by casting the solution of an amphiphilic polymer and a hydrophobic polymer under humid conditions. When annealing the honeycomb-patterned films prepared from an amphiphilic copolymer and poly(bisphenol A carbonate), we obtained a variety of mesoscale structures, depending on the heating temperatures. We revealed that these microstructures were formed by using the phase-separation structures in the self-organized honeycomb-patterned films. These micropatterns can be utilized for the template for microelectrodes, superhydrophobic surfaces, photonic crystals, and as a substrate for tissue engineering.