To make some MF.MS devices such as sensors and actuators be useful in the medical application, it is required to integrate this devices with power or sensor lines and to keep the hole devices biocompatible. Integrating micro machined sensors and actuators with conventional copper lines is incompatible because the thin copper lines are not easy to handle in the mass production. To achieve the compatibility of wiring method between MEMS devices, we developed the thin metal film deposition process that coats micropattered thin copper films on the non silicon-wafer substrate. The process was developed with the custom-made three-dimensional thin film sputter/evaporation system. The system consists of process chamber, two branch chambers, substrate holder unit and linear/rotary motion feedthrough. Thin metal film was deposited on the biocompatible polymer, polyurethane (PellethaneR) and silicone, catheter that is 2 mm in diameter and 1,000 mm in length. We deposited Cr/Cu and Ti/Cu layer and made a comparative study of the deposition processes, sputtering and evaporation. The temperature of both the processes were maintained below 100°C, for the catheter not melting during the processes. To use the films as signal lines connect the signal source to the actuator on the catheter tip, we machined the films into desired patterns with the eximer laser. In this paper, we developed the thin metal film deposition system and processes for the biopolymeric substrate used in the medical MEMS devices.