In this work the authors present results from thermal nanoimprint lithography patterning of high density arrays of circular holes with 100 nm diameters at 300 nm pitch, or with 50 nm diameters at 100 nm pitch, throughout an area of 1 cm(2). They demonstrate the fabrication of dense gigabit magnetic nanodot arrays using polymethyl methacrylate and polymethyl glutarimide resist bilayers and a lift-off process. The magnetic properties of these nanodot arrays are shown to be readily characterized by alternating gradient magnetometry. Several issues are addressed which arise during patterning and characterization, such as template damage induced by Au metallization, metal residue control, and nanodot diameter tuning by oxygen plasma etching. (c) 2007 American Vacuum Society.