Minimizing the deviation in x,y,z due to change in geometry

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Consider a stationary 3d measurement machine. Let us consider an object placed on an almost flat surface. This surface can be rotated about its origin to different angles. Let us say the coordinate system has been made on the rotation surface. Consider 2 cases

  1. Surface at 0 degree and we measure a circle center (part inside an object) w.r.t coordinate system established at 0 degree of surface. I get value in $x y z$.

  2. I rotate the surface to 90 degree and repeat step 1. I will get values like in step 1. However if the surface is not really flat then I will have some deviations. How can I compensate these deviations?

Thanks.