In DESFire command set see DESFire datasheet , we have some commands like ChangeFileSettings, ChangeKey, ChangeKeySettings, FormatPICC etc.
I want to configure my DESFire cards by a configuration software but I don't know any software.
There a some tools and libraries that you can use for you goal :
Anyway, a tool is provided by NXP also. But you need to first sign an NDA, and then buy it, so I think it is better to write a proprietary program for yourself.