Integrating micro-machined sensors and actuators on the conventional devices with the copper power lines was incompatible to fabricate the mass produced micro electromechanical system (MEMS) devices. To achieve the compatibility of the wiring method between MEMS parts and devices, we developed the three-dimensional sputter-evaporation system that coats micropatterned thin copper films on the surface of the MEMS element. The system consists of a process chamber, two branch chambers, the substrate holder, and a linear-rotary motion feedthrough. Thin copper film was sputtered and evaporated on the biocompatible polymer, Pellethane$^{circed{R}}$ and silicone, catheter that is 2 mm in diameter and 700 mm in length. The metal film coating technique with three-dimensional thin film sputter-evaporation system was developed to apply the power and signal lines on the micro active endoscope. In this paper, we developed the three-dimensional metal film sputter-evaporation system operated on the low temperature for the biopolymeric substrates used in the medical MEMS devices.