Correlation-based alignment is an alternative alignment method for electron beam lithography. Using complex marker patterns, such as Penrose patterns, which contain more positional information, greater alignment accuracy can be achieved. Correlation-based alignment with Penrose patterns is less susceptible to marker edge defects, such as rat bites, roughness and flagging, since many more edges contribute to determining the marker position. There are however other defects associated with fabricating markers and this paper investigates how defects that result in parts of the pattern being omitted or obscured affect the correlation process when using Penrose pattern markers. We show that in both cases severely damaged markers can be used successfully and demonstrate fabricated structures with sub-5 nm alignment using markers with up to 80% of the marker pattern missing. (C) 2008 Elsevier B.V. All rights reserved