Nanoimprint lithography (NIL) is recognized as one of the most promising candidates for the next generation lithography (NGL) to obtain sub-100 nm patterns because of its simplicity,high-throughput and low-cost. While substantial effort has been expending on NIL for producing smaller and smaller feature sizes, considerably less effort has been devoted to the equally important issue-alignment between template and substrate. A homemade prototype nanoimprint lithography enable the substrate to move towards the desired position automatically. Linear motors with 300 mm travel range and 1 μm step resolution are used as macro actuators, and piezoelectric translators with 50 μm travel range and 1 nm step resolution are used as micro actuators. In addition, the prototype provides one translation (z displacement) and two tilting motion(α and β) to automatically bring uniform intact contact between the template and substrate surfaces by using a flexure stage. As a result, 10 μm coarse alignment accuracy and 20 nm fine alignment accuracy can be achieved. Finally,some results of nanostructures and micro devices such as nanoscale trenches and holes, gratings and microlens array fabricated using the prototype tool are presented, and hot embossing lithography, one typical NIL technology, are depicted by taking nanoscale gratings fabrication as an example.