If I own 3 lots and I am selling 2 of them, will I have to pay capital gains taxes on the 2 lots I am selling?

Yes, capital gains taxes will be due.

Your basis for each lot is one-third what you paid for the three lots (on the assumption that the lots are about the same size).

If they are radically different in size, then you must pro-rate the basis based on the size of the lots.