You can extend or replace the builder used by Flex Builder 3 with extenal programs - ant is a good choice.
If you run "Flex Builder 3 standalone" (which is a minimalist Eclipse version + the Flex builder plugin) as opposed to the Flex builder plugin in a standard Eclipse, you first need to install ant support. I didn't find ant separately packaged, so I just selected the Java build environment from Help / Software Updates.
Now you can go to your project properties (Right-Click on your Project, Properties) and chose Builders. You'll notice there is a Flex Builder per default, which you cannot remove nor change. However, you can deselect it and you can add other builders.
So in your case: "add" a new builder, ant builder, select a build.xml (can be named differently), preferably from within your project folder, and set the correct targets. This will continue to use the internal IDE builder while running your ant task just before or afterwards. The ordering on the screen will be the build order, which you can change using the arrow buttons.
I used this to copy required libraries into my /lib folder, compile the Flex sources using the IDE build (which has Eclipse-integration with error messages, which a pure ant-based commandline build would miss), and copy the result to a common deploy directory, renaming the wrapper html file in this process.
For details of how to write an ant file, please refer to the ant documentation.