If the walls were not too far out of wack you can use the thin set mortar or there are special patching mortars for going over the hardibacker board as long as it isn t applied too thick.
Tiling walls that are not plumb.
Answer answer what should have been done while installing the hardibacker board on the walls is the framing studs should have been shimmed and adjusted to make sure the hardibacker board was plumb and square.
Do this prior to any tiling job.
Subway tiles are notorious for not being well made so i always tile all 3 walls at the same time so the grout joints match up on adjoining walls.
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The horizontal line assures the 3 walls are level with each other and the grout joints will line up wall to wall.
Slide a 4 foot straightedge or level over the wall in all directions to check for plumb.
Check the wall first to see if it is straight.