To merge vertices the two pieces of geometry have to be combined into one object first (select both pieces of geo then under the Mesh menu click on Combine).Once you you have the single object you can then merge the vertices by selecting both vertices and under Edit Mesh click Merge Components.
Watch out for the spacing because the merge command has a distance value in the options and if its small then the verts have to be close to or on top of each other.You can also select a whole row of verts and merge in one command if you have your merge distance value set the the correct distance.
There is also a Merge Vertices Tool under Mesh Tools.
Personally i would not use the merge option when mirroring or duplicating as you don't have much control of the final result, i would stick to a model/duplicate/combine/merge vertices workflow for better results with more control ect.
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Last edited by jsprogg; 31-08-2014 at 03:32 PM.