I have been looking at the FileSystemObect in the last day so just knocked this up, which should do the trick.
Sub DeletePDFs(ByVal TopDirectory As String)
Dim fSys As FileSystemObject
Dim TopFolder As Folder
Dim SubFldr As Folder
Dim fl As File
Set fSys = New FileSystemObject
If fSys.FolderExists(TopDirectory) Then
Set TopFolder = fSys.GetFolder(TopDirectory)
For Each fl In TopFolder.Files
If Right(fl.Name, 4) = ".pdf" Then
For Each SubFldr In TopFolder.SubFolders
MsgBox "No Directory like '" & TopDirectory & "'"
DeletePDFs "H:\Test Top Folder"
But PLEASE test it on something unimportant until you are satisfied it does what you want OK. This cannot be Undone !!