An exemplary alignment apparatus can align a first layer with a second layer. The first layer has a first alignment pattern. The second layer has a second alignment pattern. The alignment apparatus includes a supporting device for supporting the first layer and the second layer, a light pervious reference plate, and a viewing and adjusting mechanism. The light pervious reference plate has a first reference pattern spatially corresponding to the first alignment pattern on the first layer, and a second reference pattern spatially corresponding to the second alignment pattern on the second layer. The viewing and adjusting mechanism is adapted for assisting a human operator to align the first reference pattern with the first alignment pattern and the second reference pattern with the second alignment pattern.