A true "low-level" format is something you can't do, and is somewhat of a misnomer.
HDDs these days are low-level formatted at the factory, and their layout is quite sophisticated, and can't be changed (unlike the "old-days")
What amsquerades as a low-level format these days is often (and more correctly) termed a "zero fill". What a zero-fill does is to rewrite all the user sectors (there are sectors inaccessible to users, which contain manufactuers data) of the drive back to zeroes (ie blanks them out), and restore the drive to how it was when it left the factory. It removes eveything, including partitions.
There is nothing to beware of, but you must not use this utility on any drive other than the one it was designed for - usually restricted to the particular manufacturers drives.