Can I re-format OS X drive without removing it from my MacBook Pro?
You don’t need to remove the HDD and no need for second Mac. 


Boot the MacBook Pro from the USB stick (that you made with OS X El Capitan 10.11)
Using Disk Utilities in the Tools menu, you can reformat the hard drive as part of the installation process. 


To boot using the USB, restart your MacBook and press and hold the Option key and Select the USB drive to boot.

Note: you are operating (using OS X) from the USB