Any software that could create the atom configuration used in the fdf file?

Is there any software that could generate the atom configurations used in the .fdf files? I am currently using wxDragon to convert the .cif file, but it would automatically reduce the atom number by taking advantage of symmetry. Besides, wxDragon seems doesn’t allow me to modify the structure.
I am wondering what the mainstream tools for this kind of job?

There are many tools you can use for that. Depending on the kind of systems you are working with, you may find one of them better suited for you. Here are a few pointers and this is definitely not exhaustive:

If you prefer a more programmatic approach, there is also OpenBabel: Open Babel.