Merging Vertices
When merging vertices, review and change the tolerance value, if necessary.
Set the value to a reasonable value based on the maximum distance that separates the vertices you want to merge, plus a small tolerance (say 1/10th to 1/5th of the measured value). If the tolerance is too high, inadvertent merging of neighboring vertices can occur, especially when choosing to merge based on the active model. The safest way to merge vertices is to select the required vertices, and use the Selected set only option in the merge options.

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Select the free edges by clicking the green box in the
Diagnostics slide out.
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Click
(Select Attached Vertices) to select the vertices that are attached to the selected edges.
Alternatively, use the
(Select Zone) tool to select the appropriate vertices.
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Set the merge options:
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Click
(Merge adjacent vertices/duplicatet faces) to merge the selected vertices.


If you set the tolerance too low, either no or partial merging would take place. However, any unmerged vertices would remain in the selected set allowing for further merging with a revised tolerance value.
The vertex merging scheme uses a lowest vertex number approach, which means it always merges the highest vertex number (slave vertex) to the lower number (master vertex) within the specified tolerance distance.