Hello. My knowledge on this topic may be a bit out of date but... as far as i understand, there really isn't a user-available method to "low level format" a drive. That sort of formatting is only done at the factory. All that a user can generally do is use drive software to "zero-fill" the drive / mark bad sectors for avoidance while remapping to spare sectors.
When my Maxtor drive began failing, i had to get and use the PowerMax software to zero-fill the drive about six times before the bad sectors were all remapped. i don't know if that software is compatible with your drive, or usable across USB, but if it is, it may solve your problem. (The executable can be found at the Maxtor website.) Or, perhaps the Ranish 'Partition Manager' may work, although i found it incomprehensible to use and thus wouldn't be able to help you with it.