What you need:

1. Reconfigurable part: all of them are blue, they are only armor, cores and control cabins cannot be reconfigured
2. Junk parts, fragments of parts alteration, and/or the remains from the transformation component (junk parts can be any armor parts....even cores and control cabins)
3. Precise Reconfiguration Tool (this one is optional)

The steps into reconfiguring your part.                                          
1. Press F2 and click the button shown here:

After you click that button, you will come to this window:

This is where you do all your reconfiguration.

2. Place  the item you want to reconfigure in #1

3. Add your junk parts, fragments, or remains in #5.

4.When you reach the max number (or slightly over) in #3 or #4 (depends on if you want precise or regular) or fill #5 full, press #6.

5. Enjoy your part. If you did it properly the part will be bound and the title will be orange: