What is the subfloor? Wood or concrete?
If its wood then we'll carry on. If its concrete and there's a CBU, then its a tear out.
Judging by the photo, I don't think a 1/2" notch trowel would even work as it sits now.
If you could try to scrape the ridges down without damaging the mat wire, that would be the first step.Then skim coat with thinset.
As you are laying large format stone your going to want to get the underlayment (screed layer) as flat as possible. This may require additional skim coats of thinset or an SLC layer. Use a long straight edge to see where the high or low spots are and fill as necessary.
If you think the floor is flat enough the way it is and you have taken off the high ridges, you could proceed setting the stone with a medium bed white thinset. This process is going to be a little more challenging to get your stone flat.
If you do it this way, make sure your getting full coverage on the stone. Pull up a few pcs as you go to make sure of your coverage's.
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