copy, paste visible cells after Auto filter- VBA

Use this code to select only visible cell

Selection.SpecialCells(xlCellTypeVisible).Select

Try to adopt a logic something similar to this....

See if this helps...

Sub WorkingWithFilteredCells()
Dim lr As Long
Dim cell As Range

lr = Cells(Rows.Count, "E").End(xlUp).Row
With Rows(1)        'Applying filter on row1
    .AutoFilter field:=5, Criteria1:="Your filter criteria here"      'Filtering column E
    If Range("E1:E" & lr).SpecialCells(xlCellTypeVisible).Cells.Count > 1 Then
        For Each cell In Range("E2:E" & lr).SpecialCells(xlCellTypeVisible).Cells   'Iterating through the visible cells only
            MsgBox cell.Address
            'the msgbox is just to demonstrate you that you are in the correct cell, remove it as it is not required in the code
            'Here will be your code which will perform an action on the visible cell only like cell.Formula="Your formula here"
        Next cell
    End If
    .AutoFilter
End With
End Sub