Well that can sometimes depend on what File System you are using, but for the most part the command fsck does the trick. Now this is normally ran at startup, but if you would like you can run it again, but keep in mind that it is normally a good idea to umount the partition before checking the filesystem on it. Here is the syntax if you would like to do this, even after it is done at startup:
#umount /dev/hd?(the ? being whatever your partition # is.)
#fsck -f /dev/hd?
that should do the trick for you.