Major defects encountered in nanoimprint lithography (NIL) process, especially particle and gap associated defects are studied in this article. Unlike in other lithography, a particle induced defect in NIL is larger than the particle itself. To remove the particles, a dry clean process for the nanostructure-patterned surface is explored. The gap-associated defect is a unique phenomenon in NIL, which is induced by the incomplete contact between mold and substrate. The pressure required to eliminate voids during the NIL process is discussed. Based on the studies, both visual particle and void associated defects free 4 in. and even larger wafers are achieved. (c) 2005 American Vacuum Society.