This paper presents a novel strategy to fabricate two-dimensional poly(3,4 ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) photonic crystals (PCs) combining electron beam lithography (EBL) and plasma etching (PE) processes. The surface morphology of PEDOT:PSS PCs after mild oxygen plasma treatment was investigated by scanning electron microscopy. The effects on light extraction are studied experimentally. Vertical extraction of light was found to be strongly dependent on the geometric parameters of the PCs. By changing the lattice type from triangular to square and the geometrical parameters of the photonic structures, the resonance peak could be tuned from a narrow blue emission at 445 nm up to a green emission at 525 nm with a full width at half-maximum of 20 nm, which is in good agreement with Bragg's diffraction theory and free photon band structure. Both finite-difference time-domain and plane wave expansion methods are used to calculate the resonant frequencies and the photonic band structures in the two-dimensional photonic crystals showing a very good agreement with the experiment results. A 2D nanopatterned transparent anode was also fabricated onto a flexible polyethylene terephthalate (PET) substrate and it was integrated into an organic light-emitting diode (OLED). The obtained results fully confirm the feasibility of the developed process of micro/nano patterning PEDOT:PSS. Engineered polymer electrodes prepared by this unique method are useful in a wide variety of high-performance flexible organic optoelectronics.