Usually, when you get that message, the system continues by offering to run Chkdsk unless you hit a key to stop it and continue booting.
If it does that when you reboot, let it run. If it doesn't, and you get to your desktop:
1. Before you start, be sure your critical files are backed up.
2. Click Computer/My Computer
3. Right click over Local Disk C: and select "Properties."
4. Click the "Tools" tab, and select "Error Checking."
5. When you start it, select the option, "Automatically fix file system errors."
When you start it, the system will tell you this option requires rebooting the system. Do it, and when Windows restarts, let it run.