A nanoimprint system and methods for separating imprinted substrates with nano-scale patterns from mold for manufacturing. Generally, the system includes means to create, monitor, and control relative movement between the mold and substrate for separation. It is capable of controlling where and when the separation happens and finishes. The relative movement may be generated by motion stages, springs, stage driven flexures, inflatable O-rings, gas flow, and other mechanical means. It may be monitored by separation force, overhead camera, and vacuum/pressures in different area of the system. The relative movement may be any combination of stages movements and movement sequences. The separation speed, direction, and force can be well controlled in the system to achieve fast and reliable separation between mold and substrate, and at the same time maintain the pattern shape and details on the consolidated imprint resist.