As stated above, entering safemode and running the checkdisk operation would be the best course of action for you to take. It depends on your computer and BIOS, but usually it is either F8 of F12 that will allow you to access the boot options. You may want to search google for your specific model's way to access the options.
Once you are in safemode, you will have one of two course of action: either running the checkdisk via the command prompt or by the windows UI. I would choose the latter first by going to my computer, right clicking your main drive and selecting properties, after which you can navigate to the tools tab and select "check now" under error checking.
Now it usually will do the checkdisk right then and there, but if it gives a prompt like "cannot check now must restart," simply click "schedule checkdisk" and restart your computer. Once you do so, you should see a black screen that looks alot like a command prompt window. Let the timer count down and let the checkdisk commence. It may take a while depending on the amount of data stored on your drive.
If you are able to use the checkdisk right in safe mode, simply let it do its thing and then restart once it has completed.
Go ahead and let us know if any of that has worked or not and we can go from there.