Can ATC tell if aircraft is being flown manually?
No, the air traffic controller cannot see the whether the autopilot is used or not.

However, in the Mode S radar and ADS-B protocols there are messages defined that contain state of the autopilot. Currently there is no requirement that this data is provided by the aircraft, but some aircraft/transponders do provide the information nevertheless. The data is not displayed to the controller though.

In some control centres the aircraft's Mode Control Panel / Flight Control Unit Selected Altitude can be displayed to the air traffic controller. The information can be used to reduce Level Busts. 

From observations of the radar track it is difficult to tell. A competent pilot will be able to maintain altitude and heading in such a way that it is difficult to see the difference from an autopilot at the resolution of the ATC display. 

There are circumstances where the pilot is required to use the autopilot, especially to keep separation from other aircraft. In Reduced Vertical Separation Minima (RVSM) airspace the vertical separation is 1000 ft between Flight Level 290 and FL410. The aircraft must be flown using the autopilot in this airspace to ensure the flight levels are adhered to strictly.