If you wish to use Auto Merge, shown below, you must specify a merge Tolerance. Pointwise will then apply the Connector-Connector, Node-Node and Node-Connector pair merging operations all at once with that tolerance to try to create a watertight mesh.

The Merge panel is used to remove coincident and overlapping connectors.
Use Auto Merge to perform global connector, node and connector-node merging.


Merging Connectors

Fault Tolerant Meshing Using Grid Merge

Dealing With Dirty Geometry - Fault Tolerant Meshing