From an Ubuntu perspective:

There's a few different ways to do this, but this is the one that I have most luck with. Open a terminal and type
Code:
 sudo touch /forcefsck
and then reboot the system.

The program you use that's like chkdsk is e2fsck. It has a ton of options but in order to actually check the disk it needs it to be unmounted or it can hose the file system, which it will warn you of if you try to do it manually. Doing it this way, the disk is checked and cleaned before it is mounted at boot.