Use fsck (File System ChecK). This is the ugly price we pay for not having a modern journalling filesystem. fsck can take a darn long time on a big drive like the 100GB one I just put in my most recent e-smith server.
Generally, fsck alone will fix the problem, but things can get pretty botched up from time to time. You can use "fsck -y" if you're brave, or have good backups (generally, having backups makes you brave...) The "-y" tells fsck to go ahead and try to fix everythign without asking you first. Usually OK, but can occasionally lay waste to a filesystem. Did I mention good, frequent backups are important?