In this paper, a new fabrication approach of a polymer micro via hole array on a large area substrate is presented by a combination of hot embossing and indentation processes. Polymer via holes were formed by hot embossing, and opened by an indentation process. An aluminum alloy buffer layer, as a receptor of pins on a stainless steel mold due to the low hardness of aluminum, was used to support a polymer sheet. The via hole array was fabricated by a sequential process of hot embossing and indentation. Polymer micro via hole arrays 100 μm to 1.0 mm in diameter were fabricated on a 10 cm × 10 cm area successfully. This facile approach is promising for a low-cost mass fabrication of polymer micro via arrays on a large area substrate.