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 2×1 reconstructed Si(100) 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°C, where normally carbon contaminants result in the formation of SiC clusters on the surface at annealing temperatures below 950°C. Reactive ion etched marker structures with an etch depth of 60nm and a typical lateral dimension of only 150nm survive a 900°C flash anneal.