You can use Linux fsck (check and repair a Linux file system) program. However normal fsck looks for ext2 or ext3 file system. Use dosfsck program that check and repair MS-DOS file systems.

It verifies the consistency of MS-DOS file systems and optionally tries to repair them. For example, run dosfsck on a MS-DOS formatted floppy disk:

# dosfsck /dev/fd0

The following file system problems can be corrected using this program:

• FAT contains invalid cluster numbers.
• Directories with a large number of bad entries (probably corrupt). The directory can be dropped.
• Files . and .. are non-directories.
• Directories . and .. in root directory. They are dropped.
• Bad file names. They can be renamed.
• Duplicate directory entries. They can be dropped or renamed.
• Directory . does not point to parent directory. The start pointer is adjusted.
• File contains bad or free clusters. The file is truncated etc