There has been many ways of finding out the focal plane of laser projection imaging system. However we use a new aligning way to get the optimum figure of the developed substrates through a microscope. In this paper, it is demonstrated that the range of depth of focus (DOF) changes together with the feature size in a way of positive correlation. This result can be used to figure out the shortest path to the focal plane. Thus a new way of aligning the focal plane for the LPI system is presented. We also test this system. It is found that the alignment precision is 2µm, adjustable range 2mm in the optical axis. Simultaneously the focal plane and the DOF can basically meet the demands in technical specification.