Soustraire cellules une à une, enfin presque :)

Option Explicit
Sub selfic()
Dim strFileToOpen1 As String, strFileToOpen2 As String
Dim sh As Worksheet
Dim cel As Range
Dim nfeuil As String, caddr As String, form As String
Dim p1 As String, n1 As String, p2 As String, n2 As String
Dim pos1 As Integer, pos2 As Integer

strFileToOpen1 = Application.GetOpenFilename _
(Title:="Premier classeur", _
FileFilter:="Excel Files *.xls* (*.xls*),")
strFileToOpen2 = Application.GetOpenFilename _
(Title:="Second classeur", _
FileFilter:="Excel Files *.xls* (*.xls*),")
pos1 = InStrRev(strFileToOpen1, "\")
p1 = Left(strFileToOpen1, pos1 - 1)
n1 = Right(strFileToOpen1, Len(strFileToOpen1) - pos1)
pos2 = InStrRev(strFileToOpen1, "\")
p2 = Left(strFileToOpen2, pos2 - 1)
n2 = Right(strFileToOpen2, Len(strFileToOpen2) - pos2)
For Each sh In ThisWorkbook.Worksheets
    nfeuil = sh.Name
    For Each cel In sh.Cells
    caddr = cel.Address
    form = "='" & p1 & "\[" & n1 & "]" & nfeuil & "'!" & caddr & "-'" & p2 & "\[" & n2 & "]" & nfeuil & "'!" & caddr
    cel.Formula = form
    Next cel
Next sh
End Sub

Option Explicit
Sub selfic()
Dim strFileToOpen1 As String, strFileToOpen2 As String
Dim sh As Worksheet
Dim cel As Range
Dim nfeuil As String, caddr As String, form As String
Dim p1 As String, n1 As String, p2 As String, n2 As String
Dim pos1 As Integer, pos2 As Integer
Dim str1 As String, str2 As String
Dim savedcalcmode As XlCalculation

strFileToOpen1 = Application.GetOpenFilename _
(Title:="Premier classeur", _
FileFilter:="Excel Files *.xls* (*.xls*),")
strFileToOpen2 = Application.GetOpenFilename _
(Title:="Second classeur", _
FileFilter:="Excel Files *.xls* (*.xls*),")
pos1 = InStrRev(strFileToOpen1, "\")
p1 = Left(strFileToOpen1, pos1 - 1)
n1 = Right(strFileToOpen1, Len(strFileToOpen1) - pos1)
pos2 = InStrRev(strFileToOpen1, "\")
p2 = Left(strFileToOpen2, pos2 - 1)
n2 = Right(strFileToOpen2, Len(strFileToOpen2) - pos2)
For Each sh In ThisWorkbook.Worksheets
    savedcalcmode = Application.Calculation
    Application.Calculation = xlCalculationManual
    Application.ScreenUpdating = False
    nfeuil = sh.Name
    str1 = "='" & p1 & "\[" & n1 & "]" & nfeuil & "'!"
    str2 = "-'" & p2 & "\[" & n2 & "]" & nfeuil & "'!"
    For Each cel In sh.UsedRange
        caddr = cel.Address
        form = str1 & caddr & str2 & caddr
        cel.Formula = form
    Next cel
    sh.[A1] = strFileToOpen1
    sh.[B1] = strFileToOpen2
    Application.Calculation = savedcalcmode
    Application.ScreenUpdating = True
Next sh
End Sub