In this work, we study of the effect of focused ion beam (FIB) and pre-growth treatment based on local droplet etching (LDE) techniques combination on the regular nanohole array formation on GaAs (001) surface, which can act as template for selective quantum dot formation in future. The results of the influence of the regimes of method combination on the nanohole shape and size are presented. Based on the analysis of Raman spectra, we have shown that the use of LDE-based technique makes it possible to almost restore the crystal structure of FIB-modified regions completely. The possibility of obtaining highly symmetrical, faceted by {101} and {011} planes nanoholes of various diameters and depths in selected surface points in one technological cycle is shown.