Originally Posted by MTS

I do it before the quilting.

Take some poly batting, place it behind your motif, and stitch around it to outline the flower with water solvable thread (or it you want that outline to show, then with a colored thread).
Then cut away the excess batting. Carefully. ;-)

Then you sandwich and quilt as you would normally, and when you quilt tightly around the flower, it will pop up even more.
You also can quilt detail into the flower if you want - either when you're doing the sewing the batting on, or during the FMQ process, or both.
You'll get different looks depending on what stage you do it.

No cutting of the back and stuffing required.
If you've got blocks or border strips, you can do each block separately even before they're put together.

I had the insane idea do this and ended putting trapunto under 60+ stars on a quilt.
And then handed it off to a LA to quilt.
The results were fabulous.