My USB ports stopped working a few days ago. I'm guessing it was probably connected to the unscheduled checkdisk which deleted a couple of corrupted files pertaining to a USB Disk Security program. Now the USB ports don't work like they should; my mouse lights up when I connect it to the laptop, but doesn't work. The prompt says device is not recognized, or something like that. I already uninstalled the USB Disk Security program but the ports still don't work. How do I get them working again?

Please give more info about your system specs (computer make/model, what version Windows and what SP level, what USB devices do you have)

You could try chekdisk again, with everything unplugged.

Run System File Checker:

Start > Run > SFC /ScanNow > ok

Neo Empriva Laptop
Intel Core 2 T5200
120GB HDD
2GB RAM
Windows XP SP2

USB Devices:
Mouse
Canon Printer
USB-powered speakers
USB flash drive
modem

You should first update Windows and then reinstall the USB controllers and chipset drivers. Then get back to us

See USB Device Problems? Check for Windows Updates
See How to Reinstall Your USB Controllers and Motherboard Chipset Drivers