Maya script that merges overlapping vertices within each selected mesh, using a user-specified merge threshold.

mergeVerts.py

import pymel.core as pm

# mergeVerts()
# Author: Jocelyn Kim
# Function: Mass merge overlapping vertices on selected mesh(es) under a user-specified threshold 

# 'meshes' is a list of all of the meshes in the user's selection
meshes = [x for x in [ thing for thing in pm.selected() if thing.getShape()] if x.getShape().nodeType() == 'mesh']

# UI Layout
win = pm.window (title="Merge Overlapping Vertices", rtf=True)
layout = pm.columnLayout()
threshold_text = pm.text (label='Merge Threshold', parent=layout)
threshold_field = pm.textField (tx='0.001', parent=layout)
btn = pm.button (label='MERGE', parent=layout)

def onButtonPressed (*args):
    # for every mesh in the 'meshes' list:
    for mesh in meshes:
        numVerts = mesh.verts
        oldVerts = float(len(numVerts))
        # clear selection list before starting
        pm.select (clear=True)
        # selected vertices in this mesh
        for v in numVerts:
            pm.select(v, add=True)
        # designate new threshold value based on what user specified (defaults to 0.001)
        thr = pm.textField (threshold_field, query=True, text=True)
        newThreshold = float(thr)
        # merge 'em!
        pm.polyMergeVertex (d=newThreshold)
        newVerts = float(len(mesh.verts))
        print ("MERGED for mesh: " + mesh + "~ old vert count: " + str(oldVerts) + ", new vert count: " + str(newVerts))
    pm.deleteUI(win)
        
btn.setCommand (onButtonPressed)
win.show()