Special copy programs were available that would copy the disk and remember any bad sectors.

The software would look for these sectors when the program was loading and would stop loading if an error code was not returned when accessing these sectors. These were sectors on the disk that were intentionally unreadable by the disk drive. On Atari 8-bit computers, the most common protection method was via 'bad sectors'. Special nibble-copy programs such as Locksmith and Copy II Plus could sometimes duplicate these disks by using a reference library of known protection methods when protected programs were cracked they would be completely stripped of the copy protection system, and transferred onto a standard format disk that any normal Apple II copy program could read.

The standard Apple II copy programs could not read such protected floppy disks, since the standard DOS assumed that all disks had a uniform 35-track, 13- or 16-sector layout. It was also discovered that many floppy drives did not have a fixed upper limit to head movement, and it was sometimes possible to write an additional 36th track above the normal 35 tracks. In addition, tracks did not need to be perfect rings, but could be sectioned so that sectors could be staggered across overlapping offset tracks, the most extreme version being known as spiral tracking. This allowed complex disk-based software copy protection, by storing data on half tracks (0, 1, 2.5, 3.5, 5, 6.), quarter tracks (0, 1, 2.25, 3.75, 5, 6.), and any combination thereof.

On the Apple II, unlike modern computers that use standardized device drivers to manage device communications, the operating system directly controlled the step motor that moves the floppy drive head, and also directly interpreted the raw data, called nibbles, read from each track to identify the data sectors.

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