You must have flex builder 3 installed for this.
1. Install WTP using Help->Software updates->Find and Install.
2. Create a new flex project .
3. Select the J2ee project type.
4. Select the create a combined flex using WTP option. Click Next
5. Select your tomcat home .
6.Select the location of your flex.war on the next screen. (Note: You can download flex.war and flex data services from adobe.com)
7. Click finish.
Flex builder would have create all the necccessary code structure and xml files create for you
To create a simple remote object project follow this tutorial.
There goes your first java enabled flex project.
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