We propose a method of forming quantum-size emitters within a pre-defined photonic crystal in a self-aligned fashion through controlled removal of quantum well layers via selective wet-chemical etching. To demonstrate the effectiveness of our method, we take the example of a two-dimensional photonic crystal slab containing multiple quantum wells at
its center. We successfully fabricate vertically stacked quantum nanostructures (or quantum dots) well aligned with respect to the photonic crystal backbone. Micro-photoluminescence measurements performed at 78 K reveal that the radiative transition energy blue-shifts when the lateral dimension reaches less than 100 nm, which is compared with a simple modelbased on the ‘particle-in-a-box’ picture. The proposed method may find a broad range of applications in photonics and quantum optics, where the coupling between an emitter and an optical mode needs to be maximized.