Running the fsck command is pretty straightforward; you can run it on one partition/filesystem at a time, or have fsck automatically walk its way through all filesystems listed in /etc/fstab. The latter should happen if you simply issue the command itself (with no options/arguments). To specify a partition, just do, for example:
fdisk /dev/hda1
Read the fsck man page for a full description.
You might also want to boot into rescue mode from your installation CD and run fsck from there; it might be a bit safer.
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