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This paper proposes a high throughput and nanometrically-precise fabrication method of nano-and millimetric structures on the same wafer. Recent advancement of deep reactive ion etching (DRIE), with electron beam (EB) lithography provides us with nano-HARMS for a variety of applications. However in general, DRIE condition optimized for nanometric feature is incompatible with large-scale areas, because it is highly influenced by the aspect ratio and the absolute size. This paper proposes to solve this critical problem by the two-step etching method: (1) etching of nanostructure plus contour of large area, and (2) the rest. Moreover, high-throughput EB lithography is assured by writing only the contour, while keeping nanometer-order precision by grace of the simultaneous lithography of contour and nanostructure. The method proved its capability by successful fabrication of 1 μm-scale optical filters coexisting with millimeter scale (0.75 mm2) trenches.