Never used this, but I have had trouble with multiple instances so nice to learn something new.

This seems to delete only the Word created instance, by defining it using the Excel File name

[VBA]
Option Explicit

Public appXL As Excel.Application
Public xlFile As Excel.Workbook

Sub test()
Dim FName As String
FName = "md001"

Set appXL = CreateObject("Excel.Application")
Set xlFile = appXL.Workbooks.Open _
(FileName:="C:\Temp\" & FName & ".xls")
appXL.Visible = True
xlFile.Worksheets("Sheet1").Range("A2").Select
Range("a65536").End(xlUp).Offset(1, 0).Select
ActiveCell.Select
If ActiveCell = "" Then
ActiveCell.Value = "MD"
End If
ActiveWorkbook.Save
'appXL.Visible = True
xlFile.Close True
Set xlFile = Nothing
appXL.Quit
Set appXL = Nothing

Call DOSDelete(FName)

End Sub

Sub DOSDelete(ExcelName As String)
Dim objFSO As Object
Dim objDOSFile As Object
Dim objShell As Object
Dim DOSCommands As String
Dim strCommand As String

Set objFSO = CreateObject("Scripting.FileSystemObject")
Set objShell = CreateObject("WScript.Shell")

DOSCommands = "TASKKILL EXCEL.EXE-" & ExcelName

Set objDOSFile = objFSO.CreateTextFile("DOSCommands.bat", 1)
objDOSFile.Write DOSCommands
objDOSFile.Close

strCommand = "cmd /c DOSCommands.bat "

objShell.Run strCommand, 0, True
Set objFSO = Nothing
Set objShell = Nothing

End Sub


[/VBA]