We report a large-area fabrication method to prepare chiral substrates patterned with arrays of multilayer, three-dimensional nanostructures using a combination of nanoimprint lithography and glancing angle deposition. Several structures are successfully fabricated using this method, including L-shaped, twisted arc and trilayer twisted Au nanorod structures, demonstrating its generality. As one typical example, arrays of L-shaped nanostructures, consisting of two layers of orthogonally oriented Au nanorods separated by a Ge dielectric layer in the thickness direction, exhibit giant optical chirality in the infrared region with an experimentally achieved g-factor as high as 0.38. Electromagnetic simulations show that the optical chirality results from plasmon hybridization between the two orthogonal Au segments. To demonstrate scalability, a 1 cm2 chiral substrate is fabricated with uniform chiral optical property. This method combines both high throughput and precise geometrical control and is therefore promising for applications of chiral metamaterials.