If you've got the coordinates of the primary surface X,Y,Z
You can create your cylinder surface which you will get the coordinates X1, Y1, Z1 (fine mesh will be better)
Then you define a tolerance on the coordinates, needs to be large enough to capture neighbour coordinates of the cylinder
Finally you loop on each element of X, Y, Z i.e xi, yi, zi making a proximity test with the coordinates of the cylinder, and if the distance between the coordinates is beyond range, you supress them.
There may simpler/faster solutions .. but if I had to do it myself without any help that's what I would do.
