Step-and-flash imprint lithography (S-FIL®) is a promising lithography strategy for semiconductor manufacturing at device nodes below . The S-FIL 1:1 pattern transfer technology utilizes a field-by-field ink jet dispense of a low-viscosity liquid resist to fill the relief pattern of the device layer etched into the glass mask. Compared to other sub- critical dimension (CD) lithography methods, the resulting high resolution, high throughput through clustering, 3-D patterning capability, low process complexity, and low cost of ownership of S-FIL makes it a widely accepted technology for patterned media as well as a promising mainstream option for future CMOS applications. Preservation of mask cleanliness is essential to avoid the risk of repeated printing of defects. The development of mask cleaning processes capable of removing particles adhered to the mask surface without damaging the mask is critical to meet high-volume manufacturing requirements. We present various methods of residual (cross-linked) resist removal and final imprint mask cleaning. Conventional and nonconventional (acid-free) methods of particle removal are compared and the effect of mask cleaning on pattern damage and CD integrity is also studied.