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After low-level formatting is complete, we have a disk with tracks and sectors--but nothing written on them. High-level formatting is the process of writing the file system structures on the disk that let the disk be used for storing programs and data. If you are using DOS, for example, the DOS FORMAT command performs this work, writing such structures as the master boot record and file allocation tables to the disk. High-level formatting is done after the hard disk has been partitioned, even if only one partition is to be used. See here for a full description of DOS structures, also used for Windows 3.x and Windows 9x systems.
The distinction between high-level formatting and low-level formatting is important. It is not necessary to low-level format a disk to erase it: a high-level format will suffice for most purposes; by wiping out the control structures and writing new ones, the old information is lost and the disk appears as new. (Much of the old data is still on the disk, but the access paths to it have been wiped out.) Under some circumstances a high-level format won't fix problems with the hard disk and a zero-fill utility may be necessary.
Different operating systems use different high-level format programs, because they use different file systems. However, the low-level format, which is the real place where tracks and sectors are recorded, is the same.