Measuring pwm output from low side FET with oscilloscope
For the record, your LED (D2) is connected backwards. But...


Place a resistor to Vdd instead of the LED. That would provide you with a +12V square signal driven by the FET.
Connect the ground of your oscilloscope to the ground of your circuit (it is likely to already be connected, BTW).


I believe you already have a resistor in that position, so the most likely reason for the waveform you are seeing, is that the oscilloscope is shorting the FET. That is you are connecting one side to ground, when the oscilloscope itself is connected to ground. If the oscilloscope was floating, you should be able to see the signal on the resistor.