The precision and versatility afforded by scanning probe microscopy has enabled the development of a variety of methods for the facile fabrication of user-defined patterns on a variety of surfaces with nanoscale resolution.Historically, the major limitation of such scanning-probe nanolithography has been the inherently low throughput of single probe instrumentation, which has been addressed by the use of "two-dimensional" arrays of multiple probes for parallelised nanolithography. Key to the successful implementation of such arrays is a means to accurately align them relative to the substrate surface, such that all probes come into contact with the surface simultaneously upon the commencement of lithography. Here, an algorithm for the rapid, accurate and automated alignment of an array is described in the context of polymer pen lithography. This automation enables the alignment of the array of probes within minutes, without user intervention. Subsequent nanolithography of thiols on gold substrates demonstrated the generation of features over large (cm 2 ) areas with high uniformity. Example features were 66.5 AE 9.8 and 71.3 AE 9.3 nm in size across a distance of 1.4 cm, indicating any misalignment as #0.0003 . ; Tel: +44 (0)161 3068939 † These authors contributed equally to this work.