Sysinternal tools from Microsoft will help you with that especially Process Explorer. You can probably stay watching how it works or you could try this tool WinTasks 5 which seems to promise CPU logging for up to 24 hours.
Logging CPU Usage
WinTasks 5 Professional is capable of logging CPU usage per process for up to 24 hours, which is more than enough for detecting suspicious processes. WinTasks 5 Professional can also run in the background, continuously logging CPU and memory usage while consuming a minimum of system resources. To decide which processes have been active during the night, you simply launch WinTasks and open the resource statistics window. Set the time scale to 24 hours and look for deviations in the total CPU usage graph. If there are any longer periods of high CPU loads, step through all running processes using the arrow keys to find the processes that were active during that period. This gives you a good starting point for identifying unwanted processes, backdoors, Trojans, and viruses. After identifying the suspicious processes, you can simply search the Internet for the executable files to find out what each process does.
Seems like WinTasks 5 is out of date thou. You could eventually use Perfmon (builtin feature of Microsoft products). You can find how to do it on microsoft website. It's not as advanced as Vista/7 but it should do the trick.