Taiwan Photon Source is a new 3-GeV ring with characteristics of great brightness and small emittance, at present under construction at National Synchrotron Radiation Research Center (NSRRC) site in Taiwan and due to be commissioned in 2013. The positioning of the magnets is highly sensitive to alignment errors, and the entire building will be constructed half underground at depth 12 m relative to Taiwan Light Source (TLS) for stability reasons; for these reasons the survey and alignment work is confined and difficult. To position magnets precisely and quickly, a highly accurate auto-tuning girder system combined with a survey network was designed to accomplish the alignment tasks. The survey network includes a preliminary Global Positioning System (GPS) network and a laser-tracking network. The position data from the survey network define a basis for the system of motorized girders to auto-tune and improve the accuracy. The detailed survey and alignment design, simulation and preliminary data are described in this paper.