Você pode fazer isso criando uma macro:
Sub SlideMasterCleanup()
Dim i As Integer
Dim j As Integer
Dim oPres As Presentation
Set oPres = ActivePresentation
On Error Resume Next
With oPres
For i = 1 To .Designs.Count
For j = .Designs(i).SlideMaster.CustomLayouts.Count To 1 Step -1
.Designs(i).SlideMaster.CustomLayouts(j).Delete
Next
Next i
End With
End Sub