In this work, we present the results of experimental studies of the formation processes and optical properties of ordered arrays of InGaAs nanostructures obtained by deposition of quantum well material layer on the nanopatterned  GaAs surface. For GaAs nanopatterning we used our original technique based on the combination of focused ion beam treatment and local droplet etching which allows to create regular arrays of nanoholes with different  morphology. Using room-temperature photoluminescence (PL) intensity mapping we have shown that quantum well material localizes inside the created holes but position of corresponding PL peak (960–970 nm) is independent of  morphology and is determined only by the chemical composition of the deposited material. Based on low-temperature (5 K) PL measurements we conclude that inside the holes quantum well decomposes due to the difference in a  mobility of Ga and In adatoms during its material deposition with formation a “quantum well + quantum dot” system. While the quantum well PL peak locates approximately at 920 nm, the quantum dot lines lie in the wavelength range  of 930–950 nm.