A large area semiconductor element can be manufactured with high productivity, which has low electric resistance at the boundary face of a metal and a semiconductor and has excellent characteristics and reliability. A manufacturing apparatus comprises an ion irradiation means for simultaneously irradiating hydrogen ions and ions containing an element serving as a dopant of a semiconductor to a semiconductor film or a substrate in an atmosphere under reduced pressure, and a film forming means which forms a thin film or a heat treatment means which conducts a heat treatment without exposing a sample to an air. When a sample having an a-Si:H thin film is brought into a sample preparation chamber by opening a gate valve, the chamber is exhausted to have the inside pressure of 10.sup.2 to 10.sup.-3 Pa. Then, the sample is forwarded to an ion irradiation chamber from the sample preparation chamber via an intermediate chamber of which the pressure is maintained in the range of 10.sup.-3 to 10.sup.-7 Pa, and ions such as phosphous are irradiated. After the ion irradiation, a gate valve is opened to transfer the sample to the intermediate chamber, and then a gate valve is opened to forward the sample to a deposition chamber. Subsequently, Ar gas is let in to the deposition chamber and a metal film of Al/Ti is deposited by a sputtering method. After the deposition, the sample is forwarded to a sample carry-out chamber via the intermediate chamber.