You cannot fsck a mounted filesystem so when possible (subject to running applications and users) you would simply 'umount' a filesystem (provided it's not / (root) or /usr) and then fsck it.
If it's the root filesystem then I'd normally take the system down and boot from DVD
boot cdrom -s
into single user. Then fsck root and/or usr filesystems. Booting this way means the hard disk root filesystem is not mounted when running fsck as the system root is the DVD.
Doing a read-only fsck "-n" is recommended to see how much damage there is.