PC Freezes Shortly After Startup

Hello all,
My dad's computer recently had a rouge antispyware on it that was a pain to remove but I finally got it. When I rebooted after using Malwarebytes to finalize the removal the computer froze up after about 2 minutes. The mouse kept moving but nothing was responding. There were no programs running, just some of the startup programs like Spyware Doctor. I was thinking it was probably the registry or the hard drive. Anyone who could help me out would be much appreciated. Thanks in advance.