Process running for several minutes in Sleep mode
As of OS X Mountain Lion (10.8), there has been a feature called "Power Nap" that allows the Mac to periodically wake from sleep while connected to a power adapter to retrieve emails, calendar updates, iCloud syncing, or to back up to Time Machine. This would be my guess for the reason why your Mac is waking up and running during the night and not an indication of a bad process on your Mac.

If this is unwanted behavior, it's an easy setting to switch off in System Preferences > Energy Saver: 



Note that another option here is "Wake for network access" - which would be along the lines of remote or local file/printer sharing while in sleep. I would doubt this is happening since you are asleep yourself while it's occurring :-)