The present invention provides methods of protecting a surface of an aluminum nitride substrate. The substrate with the protected surface can be stored for a period of time and easily activated to be in a condition ready for thin film growth or other processing. In certain embodiments, the method of protecting the substrate surface comprises forming a passivating layer on at least a portion of the substrate surface by performing a wet etch, which can comprise the use of one or more organic compounds and one or more acids. The invention also provides aluminum nitride substrates having passivated surfaces.