about the word "smooth". Do you mean in these spots its porus and the residue is in the valleys or do you mean that the concrete has lows and highs?
If the later is the case, you need to float the concrete and screed it smooth and level or the tile will not get a good adherance.
There are many good self leveling floating material that will solve your problem.
If you mean porus areas then the thinset will take care of that.
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