I am replacing a ceramic tile floor with 3/4" T&G Brazilian Koa. I have run into a problem in removing the ceramic floor. The tile is installed in thin set cement over 3/8" cement board which in turn is nailed down and is set in thin set cement over the subfloor. I have a 0" to 1/8" layer of thin set cement remaining on the plywood subfloor after removing the top layers. Do I need to get the remaining thin set off off the plywood and if so, any ideas on how to do so?

It needs to be removed. Grinding or sanding will probably work best. Very dusty however.

I don't know how many sq. feet you have, but when I have an unpleasant chore to do I will get the biggest, meanest machine I can rent to tackle it expediently and just deal with the dust problem the best way possible. These machines are heavy and can be very aggressive so take that into consideration.

Make sure the rental guy knows you have a plywood subfloor, don't want something that may tear up the subfloor.