I am about to start my PPL soon (still flying in FSX) and I do not understand one thing. As per FAR 91.159 if my altitude is above 3000' AGL I must maintain certain altitude depending on my course, BUT what would be my reference point to know that I am above 3000' AGL? Departing airport? MEF from chart? or just look out my window? Thanks!
FAR 91.159 speaks for itself. The reference point is directly below your current location.
There are other regulations that use "AGL" (sometimes stated as "Above the surface") as a reference (see FAR 91.155 or 91.119).
As a side note, FAR 91.159 is used to mitigate the risk of midair collisions but not at the expense of prohibiting necessary close to the surface operations (e.g., helicopter EMS, telephone line patrol, crop dusting).
On bigger aircraft there's a radar altimeter that gives you precisely that (AGL). Typically the radar altimeter reading is only shown when below 2500ft or something similar.
In little planes you don't have that information.
You estimate. Using a sectional chart the MEFs are one way to go, but we should think about what the AGL figure is meant for.
For instance MEFs will include buildings, towers, anything that raises obstructions to flight.
But that's not AGL. AGL would be above the ground.
For instance there are rules on maximum speed near airports up to a certain altitude. For that I would use the airport elevation, since its meant to produce a veil around the airport with a fixed height. AGL is used to make it clear that you are not looking for MSL altitude.
If its something to do with terrain clearance then MEF for VFR and MSA for IFR flight is clearly the best option.
And there's the rule about separation from ground objects. Those are to be estimated visually and given a wide berth !