it should fsck itself when it reboots, unless your using a journaling file system, which in that case it shouldn't need it, but if in either case it did, reboot into single user mode and ...
1. Boot single-user (appending "init=/bin/sh" to the kernel
commandline accomplishes this handily)
2. When you get the root prompt, your hard disk should be mounted
readonly. If it's not mounted, mount it with the readonly option
("-o ro"). If it's mounted read-write, remount it read-only with
the remount and read-only options (pass "-o remount,ro" as an
option to mount).
3. Run fsck.