We have demonstrated simultaneous fabrication of designed defects within a periodic structure. For rapid fabrication of periodic structures incorporating nanoscale line-defects at large area, topographically assisted holographic lithography (TAHL) technique, combining the strength of hologram lithography and phase-shift interference, was proposed. Hot-embossing method generated the photoresist patterns with vertical side walls which enabled phase-shift mask effect at the edge of patterns. Embossing temperature and relief height were crucial parameters for the successful TAHL process. Periodic holes with a diameter of 600 nm at a 1 μm-pitch incorporating 250 nm wide line-defects were obtained simultaneously.