interesting use of terminology.... in the olden days (wfm & RLL), you low-level formatted a hard drive (which was blank or from a different computer) to tell the drive controller where the data is going to be written and where it's not (bad sectors, etc). once you've done this, you can then format the drive, but the data is still going to be physically within those cylinders, heads, and sectors. with IDE drives, this is done in the factory. if you have the appropriate software and know the exact model number of a drive, you can low level format a hard drive, although it's not recommended.
with flash memory, you can generally quick format (basically wipe the fat table) or format -wipe the fat table, and redefine the format type (FAT/FAT32/NTFS/etc.) and cluster size using a PC. changing the cluster size can give better performance using some sizes of cards on some cameras. i have seen some cameras using the "Low Level" format terminology to describe a non-quick format (it rewrites the formatting, but does not remap the cylinder/head/sector in the controller).
Canon has recently added 'Low Level' format option to the 1Dmk2N for SD cards only, which allows the system to mark out bad sectors, so it's truly doing a low level format.
btw - a low level format will take longer than a regular format. if you're not having read/write issues. it's best to do a regular one.