The Options panel allows you to define tolerance values on its mesh and geometry subpanels. These tolerance values include:
Field 
Description 
node tol (mesh) 
Node tolerance is essentially the resolution to which HyperMesh maintains the finite element data in the model. When you specify a node tolerance, HyperMesh considers any two nodes to be coincident if the distance between them is less than the value. 
cleanup tol (geometry) 
"Cleaning up" refers to cleaning up the CAD geometry data by equivalencing edges, deleting fillets, and eliminating extraneous vertices. The cleanup tolerance value specifies how much HyperMesh is allowed to modify the geometry in the course of "cleaning" it. Since you will approximate the geometry with a finite element mesh, you need to work with a cleanup tolerance that is less than the node tolerance used in the mesh generation. 
Since the objective is to make a finite element mesh for the geometry, the tolerance values are determined by the demands for that mesh. You need to approximate the size of the elements that make up the smallest feature of importance in your model. HyperForm attempts to make a reasonable guess at this value when you import a CAD file, and initializes the tolerances as appropriate, but without additional input it uses a cautious estimate.
Element size 
Node tolerance 
Cleanup tolerance 

min max 
min max 
0.1 
1e4 0.01 
1e4 0.01 
1.0 
1e3 0.1 
1e3 0.1 
10.0 
0.01 1.0 
0.01 1.0 
100.0 
0.1 10.0 
0.1 10.0 