You don't use AppTrap to uninstall software.
It sits in the background and waits for you to uninstall it (by dragging an application package to the Trash). It then prompts you whether to keep or delete preferences and associated files.
if I previously uninstalled softwares by naively deleting the XXX.app folder in /Applications, is there a way to find and delete the obsolete files associated with those deleted XXX.app folders, (using AppTrap)?
No, these files will remain. What you can do however is "install" the application again, and then drag it to Trash, so AppTrap will catch it.