Dense arrays of self-assembled nanoholes are fabricated in GaAs(100) surfaces by As-free oxide cleaning thermal process. The formation of pit-like structures above 500 °C occurs by congruent evaporation of GaAs in the areas where the oxides have already desorbed. Thermally etched nanoholes exhibit inverted symmetric conical shape with an average depth/base diameter ratio of 0.21. Shallow and deep nanoholes are formed with this method, their depth ranging from 2 nm to 15 nm. Metallic Indium deposited onto the etched surfaces accumulates at the bottom of the nanoholes, thus making the etched pits a convenient template for the fabrication of high density quantum dot structures.