Geometry Repair employs three tolerance values. The first job in geometry repair is to stitch the geometry together to make a water tight solid. The merge tolerance is used to judge when two points are close enough to be considered identical. If a point is within this distance of a edge then the edge is split and the point is used as an end point of both of the created edge. If two edges share the same end point and are within the merge tolerance of each other, they are considered identical. If two surfaces have the same boundary curves and their interiors are within the merge tolerance of each other, then they are considered identical.

The defeature tolerance and angle tolerance are used during the defeaturing step. If an edge is shorter than the defeature tolerance steps will be taken to remove it. For instance, if one of the edge's endpoints is only connected to one other edge and the two edges are colinear at the point then the two edges will be merged and the point removed. If two edges meet at a vertex and form an acute angle smaller than the angle tolerance then steps will be taken to remove one or the other of the edges. For instance, the two surfaces that meet at one of the edges can be merged and the edge removed.