How to measure mA level DC current at double MCU VCC
If you are doing the measurement just as a lab experiment or calibration step where the readings only need to be taken once or twice then the appropriate way to do this is with a battery operated MultiMeter to measure the voltage across your current sensing resistor. 

If on the other hand you need to be able to take readings using your MCU in a live product environment, even though that may be just a couple of readings per session, then you want to look for a specialty chip called a high side current monitor chip. These have a pair of inputs that detect the voltage drop across a high side current sense resistor and translate that voltage down to a low side output that can be scaled to your MCU input. 

There are quite a range of these devices available that have performance ratings over a wide scope with pricing proportional to the performance and features. One part that you may want to consider is the ST TSC101 part that is easy to use with few added parts.

 

(picture from above linked data sheet)