An imprinting apparatus including a plate unit, and a plurality of imprinting modules provided on a lower surface of the plate unit. Each imprinting module is self-aligned by a compliance of six degree of freedom and vertically moved along with the plate unit by a controller. The imprint module is independently self-aligned in response to surface conditions of an objective material to compensate for a relative pose error thereof, such that a pattern formed on a lower end of the imprinting module can be imprinted on an upper surface of the objective material within a predetermined unit range, and a sequence of imprinting the pattern of the imprinting module on the objective material can be variously controlled.