Measure signal from common-source N-MOSFET with ground-referenced oscilloscope
The conventional way to use a scope to measure the voltage across the R1/D2 combination in your schematic is to use two probe channels (ie Chan A and Chan B). One probe goes to each end of the combination. Then setup the scope to show A + (B inverted). This ends up showing A-B as the scope waveform. 

Modern day digital scopes may have more sophisticated "math" functions that can be performed including the difference between the two channels.