We present a simple and effective mold cleaning method for nanoimprint lithography. Polydimethylsiloxane (PDMS) prepolymer is spin-coated onto a contaminated imprint mold, thermally cured in an ambient environment, and then peeled off afterwards. Contaminants of 100 s μm to sub-50 nm sizes are effectively cleaned within one cycle. During the cleaning process, a very thin PDMS film (1–2 nm) is uniformly coated onto the mold surface, serving as a protection and anti-sticking layer.