Fault or failure of software contained in medical devices will seriously endanger users and should be considered to reduce risk. In software development process, the risk analysis and risk control are very important for software contained in medical devices. In order to promote the quality of software contained in medical devices, a website is designed to provide the operating procedure of software contained in medical devices in this paper. The configuration management of software with operation procedure is managed by website based relational database developed by PHP and MySQL. Software process model, V-mode, is applied to guide software development process and used to promote the reliability of software. Moreover, fault tree analysis and failure mode and effects analysis are used to achieve risk analysis and risk control. The risk of software contained in medical devices can be effectively reduced. Therefore, software verification and validation is also integrated to verify and validate the function of software. Integrated Cephalometric Analysis System had been used to show that proposed approach is feasible.