Registration markers are crucial in connecting scanning tunneling microscope (STM) lithographed nano- and atomic-scale devices to the outside world. In this paper we revisit an ultra high vacuum annealing method with a low thermal budget that is fully compatible with etched registration markers and results in clean 2 x 1 reconstructed Si(1 0 0) surfaces required for STM lithography. Surface contamination is prevented by chemically stripping and reforming a protective silicon oxide layer before transferring the sample to the vacuum system. This allows for annealing temperatures of only 900 degrees C, where normally carbon contaminants result in the formation of SiC clusters on the surface at annealing temperatures below 950 degrees C. Reactive ion etched marker structures with an etch depth of 60nm and a typical lateral dimension of only 150nm survive a 900 degrees C. ash anneal. (C) 2010 Elsevier B.V. All rights reserved.