In the old days, they'd take samples from different areas and see if they fuse in a a petri dish, which indicates they are the same individual. These days genetic testing is faster and easier though.

So basically you take samples from different areas and map out where the fungus matches out as genetically identical. Once you get an idea of the amount of ground surface it covers, you can estimate total mass by figuring how much fungus mass is in a given square meter of soil (or whatever) and multiplying by the total area.