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Nanoimprint Lithography presents unique opportunities for high density patterning due to its advantages of sub-10nm resolution capability and high throughput. Imprint and pattern transfer with Pillar tone template were widely studies recently. However, there are several critical issues that still remain very challenging, including fabrication of pillar templates and pattern reverse from imprint holes to nano dots array at high density. In this Paper, we will demonstrated the feasibility of imprint with hole tone template and its application in high-density nanodot array patterning. The authors have successfully demonstrated hole-tone template fabrication process and pattern transfer results with imprint pillar. The profile of imprint resist pillar was analyzed with cross-section scanning electron microscope (SEM). Pattern was transferred to underneath Co alloy thin films by ion beam milling into aligned dots with pitch of 50 nm. Magnetic dots array were investigated with SEM and M-H loop measurement. Strong perpendicular anisotropy was induced by the patterning process. Magnetic measurement reveals through ion milling process, magnetization reversal was changed from domain wall pinning dominated to Stoner-Wohlfarth coherent rotation dominated. Coercivity and Remanence change during Ion beam etching were discussed. Extendibility to ultra-high density patterning is also investigated.