A method for removing a mask in a selective area epitaxy process is provided. The method includes forming a first layer on a substrate and oxidizing the first layer. A patterned photoresist can be formed on the oxidized first layer. A portion of the oxidized first layer can then be removed using a wet chemical etch to form a mask. After removing the patterned photoresist a second layer can be epitaxially grown in a metal organic chemical vapor deposition (MOCVD) chamber or a chemical beam epitaxy (CBE) chamber on a portion of the first layer exposed by the mask. The mask can then be removed the mask in the MOCVD/MBE chamber. The disclosed in-situ mask removal method minimizes both the atmospheric exposure of a growth surface and the number of sample transfers.