As the magnetic storage industry roadmap calls for aggressive terabit/in 2 densities over the next few years, the shift from the current planar media to patterned media; grooved surfaces (discrete track media / DTM) and/or individually defined magnetic dots (bit patterned media / BPM), will be necessary. Both types of patterned media require lithography to produce the pattern on the disk and the most promising lithography candidate today is nano-imprint lithography (NIL). During the imprinting process a thin, round, transparent template made of quartz is functioned as a mold to inversely transfer the features from its surface to the patterning medium on the disks by direct contact. One issue with this technique is the high probability of defects due to repeated contact of the template with the resist before, during, and after UV radiation. Defect management through template cleaning, inspection and defect characterization is critical to preserve integrity of the process. In this paper, advanced acid-free cleaning combined with MegaSonic treatment for defect elimination is investigated for effectiveness on discrete track recording (DTR) and BPM patterned templates. For the experiments, templates containing 250KTPI (100nm track pitch) full surface DTR pattern, 450 KTPI (56nm track pitch) with narrow band DTR pattern, and 250Gdpsi (50nm track pitch) with narrow band BPM pattern are used. The effect of MegaSonic cleaning on the pattern integrity of fragile features is studied. General characterization of defect attributes is made feasible through a series of imprinting and template cleaning cycles focused on resist residues and contaminant removal. Imprinted disks are analyzed using Candela disk inspection and SEM imaging of the pattern. Template cleaning is performed using HamaTech MaskTrack TeraPure automated template cleaning system.