Fsck

The filesystem consistency check and interactive repair program. When a filesystem is not properly unmounted before a reboot or halt the filesystem must be checked and any inconsistencies repaired. This can be a lengthy process and FreeBSD has a background fsck so that the system can start while it works away at making the filesystem consistent.

If you show down improperly on Linux and know you will have to answer "yes" many times, you can simply add the -y flag which means say yes to the prompts

# fsck -y