You should run ScanDisk regularly to check the health of your hard disk – though it'll also check over other types of disk. ScanDisk can fix certain types of error.

A basic test can be conducted by running ScanDisk, clicking on the drive to be checked, and pressing Start. Multiple drives may be selected by [Ctrl]+clicking on each one. It's a good idea to have the Automatically Fix Errors checkbox ticked:

This will catch a lot of common errors, such as lost file fragments (also known as lost clusters) which often occur when a program gets itself in a knot and fails, possibly bringing down the Windows system with it. Lost clusters are parts of the disk which are marked as being in use, but which don't belong to any file. Unless they are recovered the space they occupy will be forever lost, reducing the capacity of the drive.

You may also see mention of cross-linked files. This is where two or more files are shown in the File Allocation Table (FAT) to be using the same part of the disk – clearly an impossibility, and at least one of them does not own the 'shared' section.

It is so important to run ScanDisk after a mishap that Windows 98 will run it automatically if it is not shut down properly. Even if you don't experience such problems, run ScanDisk at least once a week.

You may like to configure the program's behaviour by pressing the Advanced button which takes you here:

This dialog has two extra options over the Windows 95 version: you can now ask ScanDisk to check for duplicate filenames. You wouldn't normally be allowed to have the same name twice in a folder, but it might happen by mistake. Ticking this checkbox will make ScanDisk run slower on folders containing a large number of files.

On the bottom right is the other new option, Report MS-DOS Mode Name Length Errors. This will deal with files whose path plus filename exceeds 66 characters, which makes it impossible to open the directory in MS-DOS mode. Here is an example error report:

You may not be worried by such reports, because you can access the files through Windows 98 and in an MS-DOS box. You just can't start in MS-DOS mode and access them from there.

Of the other advanced options, the first two sections on the left are easy to understand and the settings are entirely up to you. The other three sections need more careful consideration, however.

Cross-linked files can be deleted if you are confident that you have backups of important files. If you haven't, then you may want to use advanced recovery tools or a data recovery service to try to piece together at least one good file out of the two. In such cases cross-linked files should not be deleted. Ignoring problem files should be a temporary measure only.

The same arguments apply to lost file fragments: free them up if you know you have good backups. Convert them to files and try to extract the data from them if you're in trouble. Expect to pay frightening amounts of money if you don't have the expertise to do this yourself.

In the Check Files For section, invalid filenames are those that break the rules for naming files, and may therefore be inaccessible from the DOS command line, for example. Invalid Dates and Times include files whose dates/times are in the future. The cause may be as simple as you having adjusted your system clock since the file was last used, or it may indicate something more serious. If you want ScanDisk to fix this type of error, it will delete offending files or make their date/time stamps current, prompting you back in the main dialog, ScanDisk's standard test only looks for errors in the way data has been stored on the disk – errors analogous to misprints in a book. What it doesn't check is the disk itself. Being able to read all of a book doesn't mean there aren't holes in the paper that hasn't yet been written on, or there isn't printed paper which is in bad condition and about to disintegrate.

A more fundamental test of disk health is conducted by the thorough option. This is slower than the standard scan, and so should be run less frequently unless you're investigating a problem. Under normal circumstances, once a month is sensible on PCs which are backed up regularly and are not mission-critical.