We report on the development of a soft UV-nanoimprint lithography (UV-NIL) based process to fabricate nanopatterned templates for epitaxy of site-controlled Stranski-Krastanov grown quantum dots. Surface cleaning and chemical native oxide removal processes are analyzed in detail. The quality of the surface is studied by means of scanning electron microscopy, atomic force microscopy and photoluminescence analysis. To evaluate the suitability of the process for fabricating high optical quality site-controlled quantum dots, we have investigated the photoluminescence signal of the near-surface quantum well and overgrown quantum dots. We present the successful growth of optically active, site-controlled InAs quantum dots, both in the ensemble and single-dot regime, by molecular beam epitaxy on UV-NIL patterned GaAs surfaces using only chemical cleaning prior to the growth. (C) 2010 Elsevier B.V. All rights reserved.