Use SpecialCells to delete only the rows that are visible after autofiltering:
ActiveSheet.Range("$A$1:$I$" & lines).SpecialCells _
(xlCellTypeVisible).EntireRow.Delete
If you have a header row in your range that you don't want to delete, add an offset to the range to exclude it:
ActiveSheet.Range("$A$1:$I$" & lines).Offset(1, 0).SpecialCells _
(xlCellTypeVisible).EntireRow.Delete