1. Add a new mxml application into one existed app and named it as what you want. Mine is TestApp.mxml.
2. Use the right key of your mouse to click your application listed in Flex Navigator, then open the Properties for yourappname dialog.
3. Select Flex Modules panel, “add” TestApp.mxml as a module. Do not “browse” to add TestApp.xml, you can not find it in the Select Module dialog, just edit the Source path like this “src/TestApp.mxml”. Pay attention here : you should select “Do not optimize (module can be loaded by multiple applications)” instead of the default option in order to generate a standalone SWF file.
4.Compile your application using Build Project or Builder All as you wish. Then you can find two, or more if any, SWF files displayed in bin-debug directory.